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9yle

State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac

Method: ELECTRON MICROSCOPY Dmax: 195.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin

Homo sapiens

UniProt P0CG47

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 15 DNA 2 PDB declaration: 17-meric（17） Consistent with all polymer counts Chain O； UniProt 1–76 Not recorded [histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D × 1 （A0A6P6IDI8,O14686） Retinoblastoma-binding protein 5 × 1 （Q15291） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 2-E × 2 （Q16778） DNA (145-MER) × 1 WD repeat-containing protein 5 × 1 （P61964） DNA (145-MER) × 1 Protein dpy-30 homolog × 2 （Q9C005） ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.63 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9YLE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2MBB Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex Deposited 2013-07-29 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：UNP P0CG47 residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 3 mM [U-100% 15N] GB1-UBM1, 3 mM [U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
NMR sample composition 3 mM GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
Resolution not provided
2MRO Structure of the complex of ubiquitin and the UBA domain from DNA-damage-inducible 1 protein (Ddi1) Deposited 2014-07-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：Human Ubiquitin
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298.2 K；Ionic strength (raw mmCIF value) 20；Pressure ambient
NMR sample composition 1 mM [U-100% 15N] Ub-1, 20 mM sodium phosphate-2, 7 % [U-99% 2H] D2O-3, 93 % H2O-4, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 1 mM [U-100% 15N] UBA-5, 20 mM sodium phosphate-6, 7 % [U-99% 2H] D2O-7, 93 % H2O-8, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
2MSG Solid-state NMR structure of ubiquitin Deposited 2014-08-04 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–78（72 aa） Fragment：UNP residuse 1-72
Not recorded No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions 273 K；Pressure ambient
NMR sample composition 20 mg [U-100% 13C; U-100% 15N] Ubiquitin, 30 mg [1-glucose 13C,U-100% 15N] Ubiquitin, 40 mg [2-glucose 13C,U-100% 15N] Ubiquitin, 40 % v/v MPD, 0.2 M CdCl2, 1 mg DSS, 100% H20 | 100% H20
Resolution not provided
2N13 Complex structure of MyUb (1080-1122) of human Myosin VI with K63-diUb Deposited 2015-03-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；283 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.5 mM [U-13C; U-15N] protein, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2Y5B Structure of USP21 in complex with linear diubiquitin-aldehyde Deposited 2011-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–152（152 aa） Fragment：LINEAR DIUBIQUITIN ALDEHYDE, RESIDUES 1-152
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；15% PEG8000, 0.2 M NH4SO4, pH 7.4
Resolution 2.70 Å R-free 0.279
2Y5B Structure of USP21 in complex with linear diubiquitin-aldehyde Deposited 2011-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–152（152 aa） Fragment：LINEAR DIUBIQUITIN ALDEHYDE, RESIDUES 1-152
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；15% PEG8000, 0.2 M NH4SO4, pH 7.4
Resolution 2.70 Å R-free 0.279
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Chain F 1–76（76 aa）
Chain H 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3O65 Crystal structure of a Josephin-ubiquitin complex: Evolutionary restraints on ataxin-3 deubiquitinating activity Deposited 2010-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Chain F 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；The protein complex was at 8 mg/ml in 10 mM Tris pH 7,5mm DTT. 2 microlitres drops were set up under paraffin oil. To 1.1 microlitres of precipitant (1.6 M sodium citrate pH 6.5, pH adjusted with HCl) 0.9 microlitres of protein was added, the final concentration of precipitant was therefore 0.88 M sodium citrate. For cryo crystals were passed through the 1.6 M sodium citrate pH 6.5 preciptant solution and then flash frozen in liquid nitrogen, microbatch under paraffin oil, temperature 291K
Resolution 2.70 Å R-free 0.224
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ3 Crystal structure of the A20 ZnF4 and ubiquitin complex Deposited 2010-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 9 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Chain C 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Chain D 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；292 K；0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K
Resolution 2.50 Å R-free 0.226
3OJ4 Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex Deposited 2010-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.1；292 K；0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K
Resolution 3.40 Å R-free 0.319
3OJ4 Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex Deposited 2010-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa） Fragment：Ubiquitin, UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.1；292 K；0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K
Resolution 3.40 Å R-free 0.319
3ONS Crystal structure of Human Ubiquitin in a new crystal form Deposited 2010-08-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–72（72 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；277 K；2 ul of a 10 mg/ml protein solution was mixed with 2 ul of the reservoir solution (50-56 % MPD and 8-18 % (v/v) glycerol solution in 27mM sodium citrate (pH 4.0-4.2) buffer), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.211
3PTF X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin Deposited 2010-12-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：Ubiquitin
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM TCEP) at 20 mg/ml with 1.5 ul of reservoir solution (0.1 M Tris pH 8.5 and 24% PEG 10,000), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.70 Å R-free 0.275
3PTF X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin Deposited 2010-12-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：Ubiquitin
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM TCEP) at 20 mg/ml with 1.5 ul of reservoir solution (0.1 M Tris pH 8.5 and 24% PEG 10,000), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.70 Å R-free 0.275
3ZLZ Lys6-linked tri-ubiquitin Deposited 2013-02-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：YES Mutation：YES ZN ZINC ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；20% (V/V) PEG3350 AND 0.2 M ZINC ACETATE, pH 7.4
Resolution 2.90 Å R-free 0.288
3ZLZ Lys6-linked tri-ubiquitin Deposited 2013-02-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Mutation：YES ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；20% (V/V) PEG3350 AND 0.2 M ZINC ACETATE, pH 7.4
Resolution 2.90 Å R-free 0.288
3ZLZ Lys6-linked tri-ubiquitin Deposited 2013-02-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Mutation：YES ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；20% (V/V) PEG3350 AND 0.2 M ZINC ACETATE, pH 7.4
Resolution 2.90 Å R-free 0.288
3ZNH Crimean Congo Hemorrhagic Fever Virus OTU domain in complex with ubiquitin-propargyl. Deposited 2013-02-14 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；20-30% PEG 8000, 100 MM NA CACODYLATE PH 6.5, 100 MM MG ACETATE, AND 2% N-OCTYL-BETA-D-GLUCOSIDE.
Resolution 2.30 Å R-free 0.275
4UEL UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain Deposited 2014-12-18 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；100 MM BIS-TRIS-PROPANE PH 5.8, 300 MM NABR, 21% PEG3350. 4 DEGREES CELSIUS
Resolution 2.30 Å R-free 0.234
4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
Resolution 3.69 Å R-free 0.269
4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
Resolution 3.69 Å R-free 0.269
4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
Resolution 3.69 Å R-free 0.269
4UF6 UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G Deposited 2014-12-23 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；100 MM MIB PH 5.0, 250 MM AMMONIUM ACETATE, 25% PEG 3350. 4 DEGREES CELSIUS
Resolution 3.69 Å R-free 0.269
4WHV E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B Deposited 2014-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–76（76 aa） Fragment：unp residues 1-76
Chain F 1–76（76 aa） Fragment：unp residues 1-76
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；1.04 M (NH4)2HPO4
Resolution 8.30 Å R-free 0.337
4WHV E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B Deposited 2014-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain G 1–76（76 aa） Fragment：unp residues 1-76
Chain L 1–76（76 aa） Fragment：unp residues 1-76
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；1.04 M (NH4)2HPO4
Resolution 8.30 Å R-free 0.337
4WLR Crystal Structure of mUCH37-hRPN13 CTD-hUb complex Deposited 2014-10-07 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；277 K；25% PEG 3350, 220 mM MgCl2,100 mM Bis-Tris
Resolution 2.00 Å R-free 0.227
4WUR The crystal structure of the MERS-CoV papain-like protease (C111S) with human ubiquitin Deposited 2014-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded IPA ISOPROPYL ALCOHOL × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；291 K；22% w/v PEG 4000, 15% v/v 2-propanol, 0.1M tri-sodium citrate pH 4.8 and 10% glycerol
Resolution 3.16 Å R-free 0.252
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4WZP Ser65 phosphorylated ubiquitin, major conformation Deposited 2014-11-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；30% (w/v) PEG 8000, 0.2 M ammonium sulfate
Resolution 1.90 Å R-free 0.237
4XOF Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin crystals without Zinc. Deposited 2015-01-16 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25% (w/v) PEG 1450, 50mM HEPES pH 7.0
Resolution 1.15 Å R-free 0.171
4ZFR Catalytic domain of Sst2 F403A mutant bound to ubiquitin Deposited 2015-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 77–152（76 aa） Fragment：unp residues 77-152
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2M sodium citrate tribasic diehydrate, 0.1M HEPES sodium, 20% v/v 2-propanol
Resolution 1.72 Å R-free 0.237
4ZFT Catalytic domain of Sst2 F403W mutant bound to ubiquitin Deposited 2015-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 77–152（76 aa） Fragment：unp residues 77-152
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；(0.04 M Citric acid, 0.06 M BIS-TRIS propane), 20% w/v PEG 3,350
Resolution 2.30 Å R-free 0.235
4ZFT Catalytic domain of Sst2 F403W mutant bound to ubiquitin Deposited 2015-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 77–152（76 aa） Fragment：unp residues 77-152
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；(0.04 M Citric acid, 0.06 M BIS-TRIS propane), 20% w/v PEG 3,350
Resolution 2.30 Å R-free 0.235
4ZPZ Crystal Structure of Semi-synthetic Ubiquitin with Phospho-Ser65 and Ala46Cys Deposited 2015-05-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–73（73 aa） Fragment：ubiquitin, UNP residues 1-73
Chain B 1–73（73 aa） Fragment：ubiquitin, UNP residues 1-73
Mutation：A46C, Phospho-Ser65 Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：A46C, Phospho-Ser65 Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；50 mM sodium cacodylate, 25% PEG 4000
Resolution 1.54 Å R-free 0.173
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain X 1–76（76 aa）
Chain c 1–76（76 aa）
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
Resolution 3.82 Å R-free 0.256
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain h 1–76（76 aa）
Chain m 1–76（76 aa）
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
Resolution 3.82 Å R-free 0.256
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
Resolution 2.49 Å R-free 0.304
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
Resolution 2.49 Å R-free 0.304
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
Resolution 2.49 Å R-free 0.304
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000
Resolution 2.49 Å R-free 0.304
5CAW Structure of Pediculus humanus Parkin bound to phospho-ubiquitin Deposited 2015-06-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76 exchanged to chemical probe Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2% (v/v) PEG400, 2 M NH4SO4, 0.1 M HEPES pH 7.5
Resolution 2.62 Å R-free 0.260
5CAW Structure of Pediculus humanus Parkin bound to phospho-ubiquitin Deposited 2015-06-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Mutation：G76 exchanged to chemical probe Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2% (v/v) PEG400, 2 M NH4SO4, 0.1 M HEPES pH 7.5
Resolution 2.62 Å R-free 0.260
5CRA Structure of the SdeA DUB Domain Deposited 2015-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa） Fragment：UNP residues 1-75
Not recorded SO4 SULFATE ION × 6 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Tris:HCl, 3.0 M Sodium Chloride
Resolution 2.64 Å R-free 0.236
5CRA Structure of the SdeA DUB Domain Deposited 2015-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa） Fragment：UNP residues 1-75
Not recorded SO4 SULFATE ION × 3 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Tris:HCl, 3.0 M Sodium Chloride
Resolution 2.64 Å R-free 0.236
5CVM USP46~ubiquitin BEA covalent complex Deposited 2015-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–59（59 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；3.6 M sodium formate
Resolution 1.90 Å R-free 0.197
5CVN WDR48 (2-580):USP46~ubiquitin ternary complex Deposited 2015-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；292 K；0.1 M sodium chloride, 5% ethanol, 15% MPD, 0.1 M Tris pH 8.8
Resolution 3.36 Å R-free 0.222
5CVO WDR48:USP46~ubiquitin ternary complex Deposited 2015-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；15% MPD, 0.1 M NaCl, 0.1 M HEPES, pH 7.0
Resolution 3.88 Å R-free 0.275
5CVO WDR48:USP46~ubiquitin ternary complex Deposited 2015-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；15% MPD, 0.1 M NaCl, 0.1 M HEPES, pH 7.0
Resolution 3.88 Å R-free 0.275
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0K Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, sodium chloride, PEG 6000
Resolution 2.65 Å R-free 0.238
5D0M Structure of UbE2D2:RNF165:Ub complex Deposited 2015-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded PO4 PHOSPHATE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；SPG buffer, PEG 1500
Resolution 1.91 Å R-free 0.213
5DFL Crystal structure of Ube2K~Ubiquitin conjugate Deposited 2015-08-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M di-ammonium citrate pH 5.0, 20% PEG 3350
Resolution 2.10 Å R-free 0.235
5DK8 Human ubiquitin in the P1 space group Deposited 2015-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–75（74 aa） Fragment：Ubiquitin, UNP residues 2-75
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；288 K；0.2M magnesium chloride hexahydrate, 30% w/v PEG 4000, 0.1 M Tris pH 8.5
Resolution 1.32 Å R-free 0.201
5DK8 Human ubiquitin in the P1 space group Deposited 2015-09-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–75（74 aa） Fragment：Ubiquitin, UNP residues 2-75
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；288 K；0.2M magnesium chloride hexahydrate, 30% w/v PEG 4000, 0.1 M Tris pH 8.5
Resolution 1.32 Å R-free 0.201
5E6J Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe Deposited 2015-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–75（75 aa）
Not recorded ACT ACETATE ION × 1 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；285 K；0.1 M MES, 0.1 M lithium acetate, 17% PEG 6000
Resolution 2.85 Å R-free 0.264
5E6J Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe Deposited 2015-10-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–75（75 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；285 K；0.1 M MES, 0.1 M lithium acetate, 17% PEG 6000
Resolution 2.85 Å R-free 0.264
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–76（76 aa） Fragment：UNP residues 1-76
Chain G 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–76（76 aa） Fragment：UNP residues 1-76
Chain F 1–76（76 aa） Fragment：UNP residues 1-76
Chain G 1–76（76 aa） Fragment：UNP residues 1-76
Chain H 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5EDV Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex Deposited 2015-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 1–76（76 aa） Fragment：UNP residues 1-76
Chain H 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；285 K；0.06M Tris, 0.04M Bicine, 0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2- Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 20% PEG550MME, 10% PEG20K, 8% glycerol
Resolution 3.48 Å R-free 0.303
5EMZ Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit Deposited 2015-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：F45W SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；LiSO Tris PEG-3350
Resolution 1.66 Å R-free 0.209
5EMZ Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit Deposited 2015-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Mutation：F45W SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；LiSO Tris PEG-3350
Resolution 1.66 Å R-free 0.209
5EMZ Crystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit Deposited 2015-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Mutation：F45W SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；LiSO Tris PEG-3350
Resolution 1.66 Å R-free 0.209
5EYA TRIM25 RING domain in complex with Ubc13-Ub conjugate Deposited 2015-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Li citrate, 20% PEG 3350
Resolution 2.40 Å R-free 0.228
5GJQ Structure of the human 26S proteasome bound to USP14-UbAl Deposited 2016-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain y 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 2 seconds before plunging
Resolution 4.35 Å
5GO7 Linear tri-ubiquitin Deposited 2016-07-26 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；0.2M sodium dihydrogen phosphate, 20% PEG 3350, PH 6.0
Resolution 1.80 Å R-free 0.310
5GO8 Linear tetra-ubiquitin Deposited 2016-07-26 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；0.2M Sodium acetate trihydrate, 20% PEG 3350, PH8.0
Resolution 2.21 Å R-free 0.322
5GOB Lys6-linked di-ubiquitin Deposited 2016-07-26 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；289 K；0.2M Magnesium chloride hexahydrate, 20% PEG 3350, PH5.9
Resolution 1.15 Å R-free 0.229
5GOC Lys11-linked diubiquitin Deposited 2016-07-26 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Li2SO4, 0.1M tris 8.5, 30% PEG 4000
Resolution 1.73 Å R-free 0.235
5GOD Lys27-linked di-ubiquitin Deposited 2016-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Magnesium acetate tetrahydrate, 0.1M Sodium cacodylate trihydrate PH6.5, 20% PEG 8000
Resolution 1.15 Å R-free 0.222
5GOG Lys29-linked di-ubiquitin Deposited 2016-07-27 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Potassium sulfate, 20% PEG 3350
Resolution 1.98 Å R-free 0.330
5GOH Lys33-linked di-ubiquitin Deposited 2016-07-27 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Magnesium sulfate heptahydrate, 20% peg 3350
Resolution 1.95 Å R-free 0.271
5GOI Lys48-linked di-ubiquitin Deposited 2016-07-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1M Sodium citrate tribasic dehydrate PH5.6, 20% 2-Propanol, 20%PEG 4000
Resolution 1.59 Å R-free 0.311
5GOJ Lys63-linked di-ubiquitin Deposited 2016-07-27 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1M TRIS hydrochloride PH8.5, 2.0M Ammonium phosphate monobasic
Resolution 1.55 Å R-free 0.253
5GOK K11/K63-branched tri-Ubiquitin Deposited 2016-07-27 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；0.2M MgSO4, 20% PEG 3350, 4mM CdCl2, PH6.0
Resolution 1.84 Å R-free 0.245
5H7S Structural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of the LNX1 RING domain Deposited 2016-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；0.04 M Citric acid, 0.06 M BIS-TRIS propane, pH 6.4, 20% w/v polyethylene glycol 3350
Resolution 3.49 Å R-free 0.286
5IBK Skp1-F-box in complex with a ubiquitin variant Deposited 2016-02-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 75–150（76 aa） Fragment：UNP residues 75-150
Mutation：L8G, T9A, G10R, K11T, T12A, R42I, A46S, G47R, Q49L, Q62H, K63R, H68R, R72I, L73F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM Acetate pH 4.5, 12% PEG 4000, 15% glyerol
Resolution 2.50 Å R-free 0.240
5IBK Skp1-F-box in complex with a ubiquitin variant Deposited 2016-02-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 75–150（76 aa） Fragment：UNP residues 75-150
Mutation：L8G, T9A, G10R, K11T, T12A, R42I, A46S, G47R, Q49L, Q62H, K63R, H68R, R72I, L73F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM Acetate pH 4.5, 12% PEG 4000, 15% glyerol
Resolution 2.50 Å R-free 0.240
5IFR Structure of the stable UBE2D3-UbDha conjugate Deposited 2016-02-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；200mM tripotassium citrate, 20% PEG 3350
Resolution 2.20 Å R-free 0.243
5J8P Lys27-linked diubiquitin Deposited 2016-04-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.2M magnesium acetate tetrahydrate, 0.1M sodium cacodylate trihydrate, pH 6.5, 20% PEG 8000
Resolution 1.55 Å R-free 0.295
5JBV Lys27-linked triubiquitin Deposited 2016-04-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded NO3 NITRATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；291 K；20% (w/v) PEG 3350, 4mM CdCl2, pH 5.9, 200mM Mg(NO3)2
Resolution 2.10 Å R-free 0.306
5JBY Lys27-linked triubiquitin Deposited 2016-04-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–76（76 aa）
Chain C 1–76（76 aa）
Chain E 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (w/v) PEG 3350, 4mM CdCl2, pH 5.9, 200mM Mg(NO3)2
Resolution 1.99 Å R-free 0.308
5JG6 APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive multiubiquitination and Ubiquitin chain elongation by APC/C Deposited 2016-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 76–154（79 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium acetate, 0.1 M Sodium acetate pH 4.6, 33% PEG4000
Resolution 2.00 Å R-free 0.220
5JG6 APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive multiubiquitination and Ubiquitin chain elongation by APC/C Deposited 2016-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 76–154（79 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium acetate, 0.1 M Sodium acetate pH 4.6, 33% PEG4000
Resolution 2.00 Å R-free 0.220
5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M CHES (pH 9.5) 1.0M sodium citrate
Resolution 2.90 Å R-free 0.285
5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M CHES (pH 9.5) 1.0M sodium citrate
Resolution 2.90 Å R-free 0.285
5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M CHES (pH 9.5) 1.0M sodium citrate
Resolution 2.90 Å R-free 0.285
5JP3 Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin Deposited 2016-05-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M CHES (pH 9.5) 1.0M sodium citrate
Resolution 2.90 Å R-free 0.285
5JTJ USP7CD-CTP in complex with Ubiquitin Deposited 2016-05-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.05 M Calcium chloride, 0.1 M MES pH 6.0 and 45% PEG 200
Resolution 3.32 Å R-free 0.209
5JTJ USP7CD-CTP in complex with Ubiquitin Deposited 2016-05-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–76（76 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.05 M Calcium chloride, 0.1 M MES pH 6.0 and 45% PEG 200
Resolution 3.32 Å R-free 0.209
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Chain F 1–76（76 aa）
Chain H 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5JTV USP7CD-UBL45 in complex with Ubiquitin Deposited 2016-05-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Chain H 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M K chloride, 0.05 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate
Resolution 3.31 Å R-free 0.269
5K9P Ser20 phosphorylated ubiquitin Deposited 2016-06-01 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；45% (w/v) PEG 400, 100 mM tris-HCl
Resolution 1.55 Å R-free 0.219
5KGF Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution Deposited 2016-06-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain M 1–76（76 aa）
Chain O 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；High concentration NCP-ubme/GST-53BP1 complex at 200 mM salt was diluted just prior to grid freezing.
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Plunged into liquid ethane-propane (FEI VITROBOT MARK III)
Resolution 4.54 Å
5KHY Crystal structure of oxime-linked K6 diubiquitin Deposited 2016-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–73（73 aa）
Chain B 1–75（75 aa）
Mutation：Unnatural aminoxylysine amino acid at position 6 Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：unnatural residue 76 oxime linked to chain A ZN ZINC ION × 10 ETA ETHANOLAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；PEG 3350, Zinc acetate
Resolution 3.50 Å R-free 0.331
5KYC Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin (malonate bound) Deposited 2016-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded MLA MALONIC ACID × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；292 K；8% tacsimate pH 4.0, 20% PEG3350
Resolution 1.43 Å R-free 0.192
5KYD Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin Deposited 2016-07-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；0.2M Ammonium fluoride, 20% PEG3350
Resolution 1.62 Å R-free 0.213
5KYE Crystal structure of USP7 catalytic domain [H294E] mutant in complex with ubiquitin Deposited 2016-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5, 25% PEG3350, 0.2M Ammonium acetate
Resolution 1.97 Å R-free 0.223
5KYE Crystal structure of USP7 catalytic domain [H294E] mutant in complex with ubiquitin Deposited 2016-07-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5, 25% PEG3350, 0.2M Ammonium acetate
Resolution 1.97 Å R-free 0.223
5KYF Crystal structure of USP7 catalytic domain [L299A] mutant in complex with ubiquitin Deposited 2016-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M HEPES pH 7.5, 25% PEG3350
Resolution 1.45 Å R-free 0.185
5L8H Structure of USP46-UbVME Deposited 2016-06-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.96M Sodium Citrate pH7.5 and 0.1mM zinc chloride Cryo - 20% Glycerol
Resolution 1.85 Å R-free 0.194
5L8W Structure of USP12-UB-PRG/UAF1 Deposited 2016-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–75（75 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；3.2% PEG4000, 0.1mM MMT pH6.5, 0.1 mM TCEP. Cryo- 30% Glycerol
Resolution 2.79 Å R-free 0.259
5L9T Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with E2 UBE2S poised for polyubiquitination where UBE2S, APC2, and APC11 are modeled into low resolution density Deposited 2016-06-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 22 PDB declaration: 22-meric
Chain S 77–153（77 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
5LN1 STRUCTURE OF UBIQUITYLATED-RPN10 FROM YEAST; Deposited 2016-08-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain U 77–152（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION, RECRYSTALLIZATION；pH 6.5；292 K；12% (W/V) PEG 20000, 0.1M MES PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K
Resolution 3.14 Å R-free 0.248
5LRV Structure of Cezanne/OTUD7B OTU domain bound to Lys11-linked diubiquitin Deposited 2016-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain C 1–75（75 aa）
Mutation：K11X Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M phosphate citrate (pH 4.2), 20% (w/v) PEG 8K, 0.2 M sodium chloride
Resolution 2.80 Å R-free 0.244
5LRW Structure of Cezanne/OTUD7B OTU domain bound to ubiquitin Deposited 2016-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium acetate (pH 4.8), 6% (w/v) PEG 6K
Resolution 2.00 Å R-free 0.217
5LRW Structure of Cezanne/OTUD7B OTU domain bound to ubiquitin Deposited 2016-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium acetate (pH 4.8), 6% (w/v) PEG 6K
Resolution 2.00 Å R-free 0.217
5LRX Structure of A20 OTU domain bound to ubiquitin Deposited 2016-08-22 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0.1 M MES/imidazole (pH 6.5), 7% (w/v) PEG 8K, 20% ethylene glycol
Resolution 2.85 Å R-free 0.246
5LRX Structure of A20 OTU domain bound to ubiquitin Deposited 2016-08-22 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Mutation：G76X Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0.1 M MES/imidazole (pH 6.5), 7% (w/v) PEG 8K, 20% ethylene glycol
Resolution 2.85 Å R-free 0.246
5M93 Crystal structure of SdeA-modified ubiquitin. Deposited 2016-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 76–152（77 aa）
Mutation：M1S SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M sodium acetate pH 4 - 5.5, 0.2M lithium sulfate and 30% PEG 8000
Resolution 1.79 Å R-free 0.231
5M93 Crystal structure of SdeA-modified ubiquitin. Deposited 2016-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 76–152（77 aa）
Mutation：M1S SO4 SULFATE ION × 1 RIB alpha-D-ribofuranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M sodium acetate pH 4 - 5.5, 0.2M lithium sulfate and 30% PEG 8000
Resolution 1.79 Å R-free 0.231
5M93 Crystal structure of SdeA-modified ubiquitin. Deposited 2016-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 76–152（77 aa）
Mutation：M1S RIB alpha-D-ribofuranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M sodium acetate pH 4 - 5.5, 0.2M lithium sulfate and 30% PEG 8000
Resolution 1.79 Å R-free 0.231
5MNJ Structure of MDM2-MDMX-UbcH5B-ubiquitin complex Deposited 2016-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 77–152（76 aa）
Not recorded ZN ZINC ION × 4 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Tris-HCl, pH 8.5, 0.175 M Li2SO4 and 16-20 %(v/v) PEG 3350
Resolution 2.16 Å R-free 0.231
5MNJ Structure of MDM2-MDMX-UbcH5B-ubiquitin complex Deposited 2016-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 77–152（76 aa）
Not recorded ZN ZINC ION × 4 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Tris-HCl, pH 8.5, 0.175 M Li2SO4 and 16-20 %(v/v) PEG 3350
Resolution 2.16 Å R-free 0.231
5N2W WT-Parkin and pUB complex Deposited 2017-02-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 CL CHLORIDE ION × 1 TMO trimethylamine oxide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100mM Tris pH 8.5, 200mM TMAO, PEG MME 2000
Resolution 2.68 Å R-free 0.243
5N38 S65DParkin and pUB complex Deposited 2017-02-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100mM Tris pH 8.5, 200mM TMAO, PEG MME 2000
Resolution 2.60 Å R-free 0.236
5NL5 Crystal structure of Zn1.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：E16V ZN ZINC ION × 3 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2
Resolution 1.96 Å R-free 0.237
5NL5 Crystal structure of Zn1.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：E16V ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2
Resolution 1.96 Å R-free 0.237
5NL5 Crystal structure of Zn1.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/1.3 mM E16V hUb Deposited 2017-04-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES pH 6.5-7.0, 70 mM Zn(CH3COO)2
Resolution 1.96 Å R-free 0.237
5NLJ Crystal structure of Zn3-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 4 ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 70 mM Zn(CH3COO)2 and 20% v/v TFE.
Resolution 1.53 Å R-free 0.240
5NLJ Crystal structure of Zn3-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 1 ZN ZINC ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1 ETF TRIFLUOROETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 70 mM Zn(CH3COO)2 and 20% v/v TFE.
Resolution 1.53 Å R-free 0.240
5NLJ Crystal structure of Zn3-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM E16V hUb Deposited 2017-04-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa）
Mutation：E16V ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22-30% (w/v) PEG 1450, 50 mM HEPES, 70 mM Zn(CH3COO)2 and 20% v/v TFE.
Resolution 1.53 Å R-free 0.240
5NVG Thr12 Phosphorylated Ubiquitin Deposited 2017-05-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；291.15 K；20% (v/v) ethanol, 20% (w/v) PEG-1000, 0.1M Phosphate-citrate pH 4.2
Resolution 1.07 Å R-free 0.167
5O44 Crystal structure of unbranched mixed tri-Ubiquitin chain containing K48 and K63 linkages. Deposited 2017-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–74（74 aa）
Chain C 1–74（74 aa）
Chain D 1–76（76 aa）
Chain F 1–76（76 aa）
Mutation：Deleted for Gly 75 and Gly 76 Mutation：Deleted for Gly 75 and Gly 76 Mutation：K48R Mutation：K48R SO4 SULFATE ION × 18 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.3M MgSo4 and 100mM MES monohydrate pH 6.5
Resolution 3.14 Å R-free 0.254
5O6T BIRC4 RING in complex with dimeric ubiquitin variant Deposited 2017-06-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 75–150（76 aa）
Chain D 75–150（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；291 K；0.1 M NaHEPES pH 7.5, 1.4 M tri-Na citrate
Resolution 1.57 Å R-free 0.183
5OHK Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (high resolution) Deposited 2017-07-17 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；291 K；10% (w/v) PEG 20000, 0.1 M sodium citrate pH 5.4, 0.2 M lithium sulfate
Resolution 2.34 Å R-free 0.261
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 1–76（76 aa）
Chain K 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 1–76（76 aa）
Chain K 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 1–76（76 aa）
Chain N 1–76（76 aa）
Not recorded 15P POLYETHYLENE GLYCOL (N=34) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 1–76（76 aa）
Chain N 1–76（76 aa）
Not recorded 15P POLYETHYLENE GLYCOL (N=34) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 1–76（76 aa）
Chain M 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 1–76（76 aa）
Chain M 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHL K6-specific affimer bound to K6 diUb Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain O 1–76（76 aa）
Chain P 1–76（76 aa）
Not recorded 15P POLYETHYLENE GLYCOL (N=34) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；32.5%PEG 2K MME 200mM Ammonium Acetate 0.1M Tris pH 8.5
Resolution 2.50 Å R-free 0.227
5OHN Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low resolution) Deposited 2017-07-17 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；20% (w/v) PAA 5100 Na, 100 mM Hepes pH 8.0, 2.5% (v/v) glycerol
Resolution 3.60 Å R-free 0.253
5OHN Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low resolution) Deposited 2017-07-17 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；20% (w/v) PAA 5100 Na, 100 mM Hepes pH 8.0, 2.5% (v/v) glycerol
Resolution 3.60 Å R-free 0.253
5OHP Crystal structure of USP30 (C77A) in complex with Lys6-linked diubiquitin Deposited 2017-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.73 M sodium citrate, 0.1 M Hepes pH 7.0
Resolution 2.80 Å R-free 0.249
5TOF Room temperature structure of ubiquitin variant u7ub25 Deposited 2016-10-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–152（78 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1ul protein solution at 20 mg/ml (20 mM Tris pH 8.0, 150 mM NaCl), 1ul crystallization solution (0.1 M citric acid pH 4.6, 2.6 M ammonium sulfate)
Resolution 1.12 Å R-free 0.175
5TOG Room temperature structure of ubiquitin variant u7ub25.2540 Deposited 2016-10-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 75–152（78 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1ul protein solution at 10 mg/ml (20 mM Tris pH 8.0, 150 mM NaCl), 1ul crystallization solution (0.1 M citric acid pH 4.2, 2.2 M ammonium sulfate)
Resolution 1.08 Å R-free 0.121
5TOG Room temperature structure of ubiquitin variant u7ub25.2540 Deposited 2016-10-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 75–152（78 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1ul protein solution at 10 mg/ml (20 mM Tris pH 8.0, 150 mM NaCl), 1ul crystallization solution (0.1 M citric acid pH 4.2, 2.2 M ammonium sulfate)
Resolution 1.08 Å R-free 0.121
5TUT UbcH5a-Ub isopeptide conjugate Deposited 2016-11-07 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；Hampton PEG/Ion F10
Resolution 2.60 Å R-free 0.243
5UJL Representative 1-conformer ensembles of K27-linked Ub2 from RDC data Deposited 2017-01-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：residues 1-76
Chain B 1–76（76 aa） Fragment：residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；296 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR measurement conditions pH 6.8；296 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition 150 uM [U-99% 15N] K27-diubiquitin, Distal Ub is 15N-labelled Proximal Ub is not enriched, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 150 uM [U-99% 15N] K27-diubiquitin, Distal Ub is not enriched Proximal Ub is 15N-labelled, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
5UJN Representative 2-conformer ensembles of K27-linked Ub2 from RDC data Deposited 2017-01-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；296 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition 150 uM [U-99% 15N] distal K27-Ub2, 20 mM NaPhosphate, 0.02 % NaN3, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 150 uM [U-99% 15N] proximal K27-Ub2, 20 mM NaPhosphate, 0.02 % NaN3, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
5ULF Crystal Structure of a UbcH5b~Ub conjugate Deposited 2017-01-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；100 mM bis-Tris pH 5.5, 150 mM ammonium sulfate, 20% PEG 3350
Resolution 1.80 Å R-free 0.261
5ULF Crystal Structure of a UbcH5b~Ub conjugate Deposited 2017-01-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；100 mM bis-Tris pH 5.5, 150 mM ammonium sulfate, 20% PEG 3350
Resolution 1.80 Å R-free 0.261
5ULH Structure of RNF165 in complex with a UbcH5b~Ub conjugate Deposited 2017-01-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Not recorded GOL GLYCEROL × 2 SCN THIOCYANATE ION × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；200 mM potassium thiocyanate, 20% PEG 3350
Resolution 1.95 Å R-free 0.217
5ULK Crystal Structure of RNF165 in complex with a UbcH5b~Ub conjugate Deposited 2017-01-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；200 mM ammonium nitrate, 20% PEG 3350
Resolution 2.38 Å R-free 0.267
5V1Y Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex Deposited 2017-03-02 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；277 K；0.1 M citric acid, pH 4.6, 20% PEG6000
Resolution 1.42 Å R-free 0.175
5V1Y Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex Deposited 2017-03-02 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；277 K；0.1 M citric acid, pH 4.6, 20% PEG6000
Resolution 1.42 Å R-free 0.175
5V1Z Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex Deposited 2017-03-02 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M sodium acetate, pH 4.6, 22.5% PEG3350
Resolution 2.00 Å R-free 0.182
5V1Z Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex Deposited 2017-03-02 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M sodium acetate, pH 4.6, 22.5% PEG3350
Resolution 2.00 Å R-free 0.182
5VEY Solution NMR structure of histone H2A-H2B mono-ubiquitylated at H2A Lys15 in complex with RNF169 (653-708) Deposited 2017-04-06 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
Resolution not provided
5VF0 Solution NMR structure of human RAD18 (198-240) in complex with ubiquitin Deposited 2017-04-06 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] RAD18, 3 mM Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM RAD18, 0.6 mM [U-100% 13C; U-100% 15N] Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.9 mM [U-15N] RAD18, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N] RAD18, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.2 mM [U-100% 15N] RAD18, 1.0 mM Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 5 % Alkyl-polyethylene glycol (C12E5)/n-hexanol mixture, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM RAD18, 0.2 mM [U-100% 15N] Ubiquitin, 25 mM MES-Bis-TRIS, 50 mM KCl, 10 uM ZnCl2, 5 % Alkyl-polyethylene glycol (C12E5)/n-hexanol mixture, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5VNZ Structure of a TRAF6-Ubc13~Ub complex Deposited 2017-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；289 K；0.05-0.3 mM sodium citrate, 100 mM bBis-Tris propane, and 17-23% PEG 3350
Resolution 3.41 Å R-free 0.294
5VNZ Structure of a TRAF6-Ubc13~Ub complex Deposited 2017-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 1–76（76 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；289 K；0.05-0.3 mM sodium citrate, 100 mM bBis-Tris propane, and 17-23% PEG 3350
Resolution 3.41 Å R-free 0.294
5VO0 Structure of a TRAF6-Ubc13~Ub complex Deposited 2017-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded ZN ZINC ION × 8 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；100-200 mM Na/K tartrate, 11-15% PEG 3350 and 100 mM bis-Tris propane pH 7.5
Resolution 3.90 Å R-free 0.299
5VZM Solution NMR structure of human Rev1 (932-1039) in complex with ubiquitin Deposited 2017-05-29 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate；Pressure 1
NMR measurement conditions pH 6.8；303 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate；Pressure 1
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Ubiquitin, 20 mM Sodium phosphate buffer, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Rev1, 3 mM Ubiquitin, 50 mM Sodium phosphate buffer, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM Rev1, 1 mM [U-100% 13C; U-100% 15N] Ubiquitin, 50 mM Sodium phosphate buffer, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5VZW TRIM23 RING domain in complex with UbcH5-Ub Deposited 2017-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；0.1 M Bis-Tris, pH 5.5, 0.2 M calcium chloride, 17% w/v PEG3350
Resolution 2.28 Å R-free 0.237
5W46 Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution Deposited 2017-06-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：S65D MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；Tris pH 8.0, magnesium chloride, PEG 3350, Hepes
Resolution 1.18 Å R-free 0.190
5W46 Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution Deposited 2017-06-09 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：S65D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；Tris pH 8.0, magnesium chloride, PEG 3350, Hepes
Resolution 1.18 Å R-free 0.190
5WFI X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin Deposited 2017-07-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded GOL GLYCEROL × 5 FMT FORMIC ACID × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；50 mM Tris, pH 7.5, 100 mM sodium chloride, 5 mM DTT, 0.2 M potassium formate, 20% PEG3350
Resolution 1.85 Å R-free 0.197
5WFI X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin Deposited 2017-07-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded GOL GLYCEROL × 5 FMT FORMIC ACID × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；50 mM Tris, pH 7.5, 100 mM sodium chloride, 5 mM DTT, 0.2 M potassium formate, 20% PEG3350
Resolution 1.85 Å R-free 0.197
5X3M crystal structure of p-Ub-S65-NH2 Deposited 2017-02-06 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Lithium Sulfate monohydrate, 0.1M HEPES pH 7.5, 25%(w/v) Polyethylene Glycol 3350
Resolution 1.82 Å R-free 0.271
5X3N Crystal structure of DiUb-K6 Deposited 2017-02-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Magnesium formate dihydrate, 20%(w/v) Polyethylene glycol 3350
Resolution 1.65 Å R-free 0.276
5X3O Crystal structure of p-DiUb-S65-COOH Deposited 2017-02-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Ammonium phosphate monobasic, 20%(w/v) Polyethylene glycol 3350
Resolution 2.19 Å R-free 0.315
5XBO Lanthanoid tagging via an unnatural amino acid for protein structure characterization Deposited 2017-03-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded TB TERBIUM(III) ION × 1 SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 100；Pressure 760
NMR sample composition 20mM HEPES, 100mM sodium chloride, 10% D2O, 0.2mM [U-99% 15N] ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20mM HEPES, 100mM sodium chloride, 0.1mM [U-99% 15N] HHR23A UBA1 Domain, 0.1 mM ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5XDP K11/48-branched teraubiquitin Deposited 2017-03-28 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；289 K；0.2M Potassium nitrate, 20% w/v Polyethylene glycol 3350
Resolution 2.38 Å R-free 0.271
5XK4 Retracted state of S65-phosphorylated ubiquitin Deposited 2017-05-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition 0.8 mM [U-98% 13C; U-98% 15N] phosphorylated ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5XK5 Relaxed state of S65-phosphorylated ubiquitin Deposited 2017-05-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：UNP residues 1-76
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition 0.8 mM [U-98% 13C; U-98% 15N] relaxed pUb, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5XPK Crystal structure of ubiquitin-k6mimic Deposited 2017-06-03 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Ammonium formate, 20% w/v PEG 3350
Resolution 2.27 Å R-free 0.310
5YIJ Structure of a Legionella effector with substrates Deposited 2017-10-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Chain D 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Chain G 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Not recorded NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PEG 1000, Tris
Resolution 3.18 Å R-free 0.275
5YIK Structure of a Legionella effector with its substrate Deposited 2017-10-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Chain D 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Chain F 1–76（76 aa） Fragment：UNP RESIDUES 1-76
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PEG 1000, Tris
Resolution 3.10 Å R-free 0.279
5YMY The structure of the complex between Rpn13 and K48-diUb Deposited 2017-10-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：K48R No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition 0.58 mM [U-13C; U-15N; U-2H] Rpn13, 20 mM MES, 0.15 M sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 77–152（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
Resolution 1.50 Å R-free 0.225
5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 77–152（76 aa）
Not recorded ZN ZINC ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
Resolution 1.50 Å R-free 0.225
5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 77–152（76 aa）
Not recorded ZN ZINC ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
Resolution 1.50 Å R-free 0.225
5YT6 Crystal structure of TAX1BP1 UBZ2 in complex with mono-ubiquitin Deposited 2017-11-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 77–152（76 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Ammonium sulfate, BIS TRIS propane
Resolution 1.50 Å R-free 0.225
5ZBU Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub Deposited 2018-02-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES monohydrate, 14% PEG 4000
Resolution 3.20 Å R-free 0.262
5ZD0 Solution structure of human ubiquitin with three alanine mutations in living eukaryotic cells by in-cell NMR spectroscopy Deposited 2018-02-22 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：L8A,I44A,V70A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 0；300 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR measurement conditions pH 0；300 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR sample composition 50 uM [U-100% 13C; U-100% 15N] human ubiquitin with three alanine mutations 1, 50 uM [U-100% 15N] human ubiquitin with three alanine mutations 2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Mutation：K48R GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
Resolution 2.60 Å R-free 0.236
6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa） Fragment：UNP residues 1-76
Mutation：K48R GOL GLYCEROL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
Resolution 2.60 Å R-free 0.236
6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–77（77 aa） Fragment：UNP residues 1-77
Mutation：M77D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
Resolution 2.60 Å R-free 0.236
6A6I Crystal structure of the winged-helix domain of Cockayne syndrome group B protein in complex with ubiquitin Deposited 2018-06-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–77（77 aa） Fragment：UNP residues 1-77
Mutation：M77D GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；28% PEG1000, 10% glycerol, 0.1 M tricine (pH 8.0), and 350 mM MgCl2.
Resolution 2.60 Å R-free 0.236
6ASR REV1 UBM2 domain complex with ubiquitin Deposited 2017-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa） Fragment：residues 1-76
Not recorded NI NICKEL (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.1 M MES pH 6.0, 10 % PEG 8000
Resolution 2.36 Å R-free 0.229
6ASR REV1 UBM2 domain complex with ubiquitin Deposited 2017-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa） Fragment：residues 1-76
Not recorded NI NICKEL (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.1 M MES pH 6.0, 10 % PEG 8000
Resolution 2.36 Å R-free 0.229
6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 76–152（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000
Resolution 2.66 Å R-free 0.263
6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 76–152（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000
Resolution 2.66 Å R-free 0.263
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 76–152（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
Resolution 2.61 Å R-free 0.294
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 76–152（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
Resolution 2.61 Å R-free 0.294
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 76–152（77 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
Resolution 2.61 Å R-free 0.294
6C16 Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2018-01-04 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 77–152（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M malic acid pH 4.5, 0.15 M sodium chloride, 27% (w/v) PEG3350
Resolution 3.27 Å R-free 0.317
6C16 Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2018-01-04 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 77–152（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M malic acid pH 4.5, 0.15 M sodium chloride, 27% (w/v) PEG3350
Resolution 3.27 Å R-free 0.317
6CP2 SidC in complex with UbcH7~Ub Deposited 2018-03-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 75–152（78 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；16% PEG 3000, 0.1 M Tris pH 9.0
Resolution 2.90 Å R-free 0.288
6DGF Ubiquitin Variant bound to USP2 Deposited 2018-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 153–226（74 aa）
Mutation：Q2C, K6C, K11R, T12C ZN ZINC ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M MES buffer pH 6, 12% (w/v) PEG3350, 0.2M sodium sulfate
Resolution 2.34 Å R-free 0.224
6EI1 Crystal structure of the covalent complex between deubiquitinase ZUFSP (ZUP1) and Ubiquitin-PA Deposited 2017-09-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 GOL GLYCEROL × 1 MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；277 K；0.2 M sodium malonate pH 5, 20 % PEG 3350
Resolution 1.73 Å R-free 0.203
6FDK Structure of Chlamydia trachomatis effector protein Cdu1 bound to ubiquitin Deposited 2017-12-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded CL CHLORIDE ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M MES pH 6.5, 12% PEG 20000
Resolution 1.60 Å R-free 0.203
6FGE Crystal structure of human ZUFSP/ZUP1 in complex with ubiquitin Deposited 2018-01-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MLI MALONATE ION × 1 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 2 FMT FORMIC ACID × 7 PEG DI(HYDROXYETHYL)ETHER × 1 NH4 AMMONIUM ION × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；4% v/v Tacsimate pH 5.0 and 12% w/v Polyethylene glycol 3,350.
Resolution 1.74 Å R-free 0.209
6FTX Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain N 1–76（76 aa）
Chain O 1–76（76 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6FX4 Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C Deposited 2018-03-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76C GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1.36M tri-Sodium citrat pH6.5, 15% (v/v) Glycerol
Resolution 2.50 Å R-free 0.239
6FX4 Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C Deposited 2018-03-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Mutation：G76C GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1.36M tri-Sodium citrat pH6.5, 15% (v/v) Glycerol
Resolution 2.50 Å R-free 0.239
6FYH Disulfide between ubiquitin G76C and the E3 HECT ligase Huwe1 Deposited 2018-03-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76C SO4 SULFATE ION × 2 ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.8M Zn SO4 0.1M Na Acetat pH 4.0
Resolution 2.91 Å R-free 0.266
6GLC Structure of phospho-Parkin bound to phospho-ubiquitin Deposited 2018-05-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 GOL GLYCEROL × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.03 M of each sodium nitrate, disodium hydrogen phosphate, ammonium sulphate, 0.1 M MOPS/HEPES-Na (pH 7.5)
Resolution 1.80 Å R-free 0.205
6GZS Structure of Chlamydia trachomatis effector protein ChlaDUB1 bound to ubiquitin Deposited 2018-07-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded GOL GLYCEROL × 1 SO4 SULFATE ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M MES (pH 6.0), 20% PEG 6000
Resolution 1.90 Å R-free 0.213
6H4H Usp28 catalytic domain variant E593D in complex with UbPA Deposited 2018-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–75（75 aa）
Chain D 1–75（75 aa）
Not recorded SO4 SULFATE ION × 1 AYE prop-2-en-1-amine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；273 K；0.1 M Citrate pH 5.0 0.8 M Ammonium Sulfate
Resolution 3.50 Å R-free 0.280
6HEI Structure of the catalytic domain of USP28 (insertion deleted) bound to Ubiquitin-PA Deposited 2018-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 77–151（75 aa）
Mutation：residue 76 replaced with PA warhead Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；22% (w/v) PEG 3350, 300 mM potassium sodium tartrate
Resolution 1.64 Å R-free 0.214
6HEK Structure of human USP28 bound to Ubiquitin-PA Deposited 2018-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 77–152（76 aa）
Chain D 77–152（76 aa）
Mutation：residue 76 replaced with PA warhead Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：residue 76 replaced with PA warhead Non-standard monomer：Yes (specific site not provided by mmCIF) PG4 TETRAETHYLENE GLYCOL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；291 K；8% (w/v) PEG 3350, 200 mM ammonium acetate and 100 mM sodium citrate pH 5.4
Resolution 3.03 Å R-free 0.237
6HPR Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub Deposited 2018-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 75–152（78 aa）
Chain D 75–152（78 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M ammonium fluoride and 15% (w/v) PEG 3350
Resolution 1.70 Å R-free 0.197
6IF1 Crystal structure of Ube2K and K48-linked di-ubiquitin complex Deposited 2018-09-18 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；Tris-HCl, polyethylene glycol 3350, ammonium acetate.
Resolution 2.47 Å R-free 0.236
6IF1 Crystal structure of Ube2K and K48-linked di-ubiquitin complex Deposited 2018-09-18 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；293 K；Tris-HCl, polyethylene glycol 3350, ammonium acetate.
Resolution 2.47 Å R-free 0.236
6ISU Crystal structure of Lys27-linked di-ubiquitin in complex with its selective interacting protein UCHL3 Deposited 2018-11-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；18% PEG 3350 (w/v), 400 mM Ca(AC)2
Resolution 1.87 Å R-free 0.264
6JB6 Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.7 A resolution Deposited 2019-01-25 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, PEG 400, magnesium chloride
Resolution 2.70 Å R-free 0.284
6JB7 Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.1 A resolution Deposited 2019-01-25 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES, PEG 400, magnesium chloride
Resolution 2.10 Å R-free 0.250
6JMA cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome Deposited 2019-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain Y 1–76（76 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6K9P Structure of Deubiquitinase Deposited 2019-06-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350
Resolution 2.05 Å R-free 0.210
6LP2 Structure of Lpg2148/UBE2N-Ub complex Deposited 2020-01-08 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；PEG 3350, potassium citrate
Resolution 2.48 Å R-free 0.233
6MSB Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Chain w 1–76（76 aa）
Not recorded ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6MSD Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Chain w 1–76（76 aa）
Not recorded ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6MSE Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Not recorded ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6MSG Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome Deposited 2018-10-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Not recorded ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6N13 UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin Deposited 2018-11-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Not recorded ZN ZINC ION × 8 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.11 mM [U-13C; U-15N; U-2H] UbcH7, 0.11 mM [U-13C; U-15N; U-2H] ubiquitin, 0.11 mM [U-2H] Parkin -residues 144-465 comprising the RING0-RING1-IBR and RING2(Rcat) domains, 0.11 mM [U-2H] phosphorylated ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6NJ9 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex Deposited 2019-01-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain L 1–76（76 aa）
Chain N 1–76（76 aa）
Mutation：G76C Mutation：G76C SAM S-ADENOSYLMETHIONINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing.
Resolution 2.96 Å
6OQ1 Crystal Structure of Branched K11/K48-Linked Tri-Ubiquitin Deposited 2019-04-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain C 1–76（76 aa）
Chain F 1–77（77 aa）
Mutation：K11R, K48C, K63R Mutation：K48R Mutation：M77D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；bis-tris, sodium chloride, PEG 3350
Resolution 2.20 Å R-free 0.230
6OQ1 Crystal Structure of Branched K11/K48-Linked Tri-Ubiquitin Deposited 2019-04-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Chain E 1–77（77 aa）
Mutation：K11R, K48C, K63R Mutation：K48R Mutation：M77D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；bis-tris, sodium chloride, PEG 3350
Resolution 2.20 Å R-free 0.230
6OQ2 NMR Structure of Branched K11/K48-Linked Tri-Ubiquitin Deposited 2019-04-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain D 1–76（76 aa）
Chain E 1–77（77 aa）
Mutation：K11R, K48R, K63R Mutation：K48R Mutation：M77D No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 120 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 100 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 60 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 110 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6PGV Human Josephin-2 in complex with ubiquitin Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 4.6；293 K；0.1 M sodium acetate pH 4.6, 0.2 M CaCl2, 22.5% (w/v) PEG 6000; microbatch under Al's Oil
Resolution 2.30 Å R-free 0.224
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 77–150（74 aa）
Chain B 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 77–150（74 aa）
Chain D 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 77–150（74 aa）
Chain F 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 77–150（74 aa）
Chain H 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain I 77–150（74 aa）
Chain J 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QK9 A dimeric ubiquitin formed by a single amino acid substitution Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain K 77–150（74 aa）
Chain L 77–150（74 aa）
Mutation：G10V Mutation：G10V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.06 M Divalents (0.3M Magnesium chloride hexahydrate, 0.3M Calcium chloride dihydrate), 50% Precipitation mix 1 (40% v/v PEG 500 MME, 20 % w/v PEG 20000), 0.1 M MES pH 6.5
Resolution 2.23 Å R-free 0.281
6QML UCHL3 in complex with synthetic, K27-linked diubiquitin Deposited 2019-02-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Mutation：M1(NLE) Non-standard monomer：Yes (specific site not provided by mmCIF) K POTASSIUM ION × 2 BR BROMIDE ION × 3 EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Drops set up in MRC 2 well, 96 well plate using a Mosquito crystallization robot. 100+100 nl drops. Best crystals: 21% PEG 3350 0.15M KBr 0.1M Bis-Tris pH 5.5 Crystals grow also in KCl and AmSO4 (0.2 M), or with PEG 200 MME. Crystals can be obtained at 4C as well.
Resolution 2.10 Å R-free 0.233
6QML UCHL3 in complex with synthetic, K27-linked diubiquitin Deposited 2019-02-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–76（76 aa）
Mutation：M1(NLE) Non-standard monomer：Yes (specific site not provided by mmCIF) K POTASSIUM ION × 3 BR BROMIDE ION × 1 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298.15 K；Drops set up in MRC 2 well, 96 well plate using a Mosquito crystallization robot. 100+100 nl drops. Best crystals: 21% PEG 3350 0.15M KBr 0.1M Bis-Tris pH 5.5 Crystals grow also in KCl and AmSO4 (0.2 M), or with PEG 200 MME. Crystals can be obtained at 4C as well.
Resolution 2.10 Å R-free 0.233
6UD0 Solution-state NMR structural ensemble of human Tsg101 UEV in complex with K63-linked diubiquitin Deposited 2019-09-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–77（77 aa）
Mutation：K63R Mutation：+D77 No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；300 K；Ionic strength (raw mmCIF value) 0.1；Pressure 1
NMR sample composition 200 uM [U-98% 15N] Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 200 uM Tsg101 UEV domain, 200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 200 uM Tsg101 UEV domain, 200 uM K63-linked diubiquitin, distal domain, 200 uM [U-98% 15N] K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 125 uM [U-98% 15N] Tsg101 UEV domain, 125 uM K63-linked diubiquitin, distal domain, 125 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 200 uM [U-98% 15N] Tsg101 UEV domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 200 uM [U-98% 15N] K63-linked diubiquitin, distal domain, 200 uM K63-linked diubiquitin, proximal domain, 20 mM potassium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
6UYI hRpn13:hRpn2:K48-diubiquitin Deposited 2019-11-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–77（77 aa）
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298.15 K；Ionic strength (raw mmCIF value) 0.11；Pressure ambient
NMR sample composition 0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM [U-13C] proximal ubiquitin, 0.72 mM distal ubiquitin, 100% D2O | 100% D2O
NMR sample composition 0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM proximal ubiquitin, 0.72 mM [U-13C] distal ubiquitin, 100% D2O | 100% D2O
Resolution not provided
6UYJ hRpn13:hRpn2:K48-diubiquitin Deposited 2019-11-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–77（77 aa）
Chain D 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298.15 K；Ionic strength (raw mmCIF value) 0.11；Pressure ambient
NMR sample composition 0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM [U-13C] proximal ubiquitin, 0.72 mM distal ubiquitin, 100% D2O | 100% D2O
NMR sample composition 0.6 mM [U-13C] Rpn13, 0.6 mM Rpn2, 0.72 mM [U-13C] proximal ubiquitin, 0.72 mM distal ubiquitin, 100% D2O | 100% D2O
Resolution not provided
6XZ1 Conjugate of the HECT domain of HUWE1 with ubiquitin Deposited 2020-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa）
Not recorded PO4 PHOSPHATE ION × 2 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.65 M Sodium phosphate monobasic, potassium phosphate dibasic, 0.1 M HEPES pH 7.5
Resolution 2.30 Å R-free 0.255
6XZ1 Conjugate of the HECT domain of HUWE1 with ubiquitin Deposited 2020-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded PO4 PHOSPHATE ION × 3 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.65 M Sodium phosphate monobasic, potassium phosphate dibasic, 0.1 M HEPES pH 7.5
Resolution 2.30 Å R-free 0.255
7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain CCC 75–152（78 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
Resolution 1.82 Å R-free 0.231
7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain FFF 75–152（78 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
Resolution 1.82 Å R-free 0.231
7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain III 75–152（78 aa）
Not recorded ZN ZINC ION × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
Resolution 1.82 Å R-free 0.231
7AHZ Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain LLL 75–152（78 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；0.1 M HEPES, 10 % w/v PEG 20000
Resolution 1.82 Å R-free 0.231
7AI0 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain CCC 75–152（78 aa）
Not recorded CL CHLORIDE ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
Resolution 1.56 Å R-free 0.185
7AI0 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1) Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain FFF 75–152（78 aa）
Not recorded CL CHLORIDE ION × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium
Resolution 1.56 Å R-free 0.185
7AI1 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2) Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain CCC 75–152（78 aa）
Not recorded CL CHLORIDE ION × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
Resolution 2.07 Å R-free 0.266
7AI1 Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2) Deposited 2020-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain FFF 75–152（78 aa）
Not recorded CL CHLORIDE ION × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad
Resolution 2.07 Å R-free 0.266
7AY2 Crystal structure of truncated USP1-UAF1 reacted with ubiquitin-prg Deposited 2020-11-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；8-13% w/v PEG3350, 0.1 M citric acid/Bis-Tris propane pH 4.1
Resolution 3.20 Å R-free 0.234
7AY2 Crystal structure of truncated USP1-UAF1 reacted with ubiquitin-prg Deposited 2020-11-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–75（75 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；8-13% w/v PEG3350, 0.1 M citric acid/Bis-Tris propane pH 4.1
Resolution 3.20 Å R-free 0.234
7CAP Cyclic Lys48-linked triubiquitin Deposited 2020-06-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；20% PEG 3350, 200 mM zinc acetate
Resolution 1.33 Å R-free 0.174
7DNI MDA5 CARDs-MAVS CARD polyUb complex Deposited 2020-12-09 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Chain G 1–76（76 aa）
Chain H 1–76（76 aa）
Chain I 1–76（76 aa）
Chain J 1–76（76 aa）
Chain K 1–76（76 aa）
Chain L 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 3.20 Å
7DNJ K63-polyUb MDA5CARDs complex Deposited 2020-12-09 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Chain G 1–76（76 aa）
Chain H 1–76（76 aa）
Chain I 1–76（76 aa）
Chain J 1–76（76 aa）
Chain K 1–76（76 aa）
Chain L 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.30 Å
7F7X Protein complex between phosphorylated ubiquitin and Ubqln2 UBA Deposited 2021-06-30 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition 20 mM HEPES, 0.15 M sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded CA CALCIUM ION × 3 AYE prop-2-en-1-amine × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
Resolution 2.78 Å R-free 0.273
7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded CA CALCIUM ION × 3 AYE prop-2-en-1-amine × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
Resolution 2.78 Å R-free 0.273
7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded CA CALCIUM ION × 2 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
Resolution 2.78 Å R-free 0.273
7JMS Structure of the Hazara virus OTU bound to ubiquitin Deposited 2020-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–75（75 aa）
Not recorded CA CALCIUM ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.3 M calcium chloride, 20% PEG 4000
Resolution 2.78 Å R-free 0.273
7LYC Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Deposited 2021-03-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0 29% PEG3350 40 mM DL-Malic acid 5 mM DTT
Resolution 2.47 Å R-free 0.276
7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0 29% PEG3350 40 mM DL-Malic acid 5 mM DTT
Resolution 2.47 Å R-free 0.276
7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Not recorded GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0 29% PEG3350 40 mM DL-Malic acid 5 mM DTT
Resolution 2.47 Å R-free 0.276
7M2K CDC34A-Ubiquitin-2ab inhibitor complex Deposited 2021-03-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–76（76 aa）
Not recorded GZM 4-[(3',5'-dichloro[1,1'-biphenyl]-4-yl)methyl]-N-ethyl-1-(methoxyacetyl)piperidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES pH 7.0 29% PEG3350 40 mM DL-Malic acid 5 mM DTT
Resolution 2.47 Å R-free 0.276
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded ZN ZINC ION × 3 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded ZN ZINC ION × 3 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–75（75 aa）
Not recorded ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 1–75（75 aa）
Not recorded ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MC9 X-RAY STRUCTURE OF PEDV PAPAIN-LIKE PROTEASE 2 bound to UB-PA Deposited 2021-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.30M MgCl2, 0.1M Tris, and 16% PEG 4k
Resolution 3.10 Å R-free 0.257
7MEY Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron Deposited 2021-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–75（75 aa） Fragment：K48C
Chain D 1–75（75 aa）
Not recorded ZN ZINC ION × 7 Z3V 2-(ethylamino)ethane-1-thiol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.67 Å
7MYF Ubiquitin variant UbV.k.1 in complex with Ube2k Deposited 2021-05-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Mutation：Q31F, G21R, T23Y, A57S, K59Q, K74E, E75F, T77F, V81I, L82S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2-0.3 M ammonium citrate dibasic, 20-25% PEG3350
Resolution 3.00 Å R-free 0.293
7MYH Ubiquitin variant UbV.k.2 in complex with Ube2k Deposited 2021-05-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Mutation：K6S, L8F, T9V, K11L, T14M, K63N, E64D, T66I, H68R, L71I, G76L GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.2 M sodium citrate tribasic trihydrate, 0.1 M Bis-Tris propane, pH 7.5, 20% PEG3350
Resolution 2.39 Å R-free 0.249
7OJE Crystal structure of the covalent complex between Tribolium castaneum deubiquitinase ZUP and Ubiquitin-PA Deposited 2021-05-14 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；8 % (v/v) Tacsimate pH 7; 22 %PEG3350
Resolution 2.05 Å R-free 0.219
7OJE Crystal structure of the covalent complex between Tribolium castaneum deubiquitinase ZUP and Ubiquitin-PA Deposited 2021-05-14 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 1 ZN ZINC ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；8 % (v/v) Tacsimate pH 7; 22 %PEG3350
Resolution 2.05 Å R-free 0.219
7OJX E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for K48-linked Ub chain synthesis Deposited 2021-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Chain E 1–76（76 aa）
Mutation：K48C ZN ZINC ION × 2 ME7 1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；Crystals were grown in: 0.2 M sodium citrate, 0.1 M Bis Tris propane 7.5 and 20 % (w/v) PEG 3350. The crystallization drops were set as a 1:1 mixture of the protein complex solution and the precipitant solution.
Resolution 2.40 Å R-free 0.236
7QO5 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the si state Deposited 2021-12-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain 9 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7RBR The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with a Lys48-linked di-ubiquitin Deposited 2021-07-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–77（77 aa）
Not recorded ZN ZINC ION × 1 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.2 M di-sodium tartrate, 20% PEG-3350,
Resolution 1.88 Å R-free 0.228
7RMA Structure of the fourth UIM (Ubiquitin Interacting Motif) of ANKRD13D in complex with a high affinity UbV (Ubiquitin Variant) Deposited 2021-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–79（79 aa）
Not recorded SO4 SULFATE ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；0.1M Li2SO4, 0.1M sodium acetate pH 4.5 and 50% PEG 400. Crystals were cryoprotected in this buffer plus 20% ethylene glycol
Resolution 2.00 Å R-free 0.246
7S6O The crystal structure of Lys48-linked di-ubiquitin Deposited 2021-09-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：K48R Mutation：Aspartic acid residue added to C terminus (D77) ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.8；289 K；50 mM acetate, 8.6% PEG2000 MME, 17.1% PEG400
Resolution 1.25 Å R-free 0.175
7UV5 The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in complex with a Lys48-linked di-ubiquitin Deposited 2022-04-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Mutation：K48R ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.2 M sodium tartrate, 15% PEG3350
Resolution 1.45 Å R-free 0.179
7W38 Structure of USP14-bound human 26S proteasome in state EA2.0_UBL Deposited 2021-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7W39 Structure of USP14-bound human 26S proteasome in state EA2.1_UBL Deposited 2021-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain u 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7W3A Structure of USP14-bound human 26S proteasome in substrate-engaged state ED4_USP14 Deposited 2021-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7W3B Structure of USP14-bound human 26S proteasome in substrate-engaged state ED5_USP14 Deposited 2021-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7W3C Structure of USP14-bound human 26S proteasome in substrate-engaged state ED0_USP14 Deposited 2021-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7W3F Structure of USP14-bound human 26S proteasome in substrate-engaged state ED1_USP14 Deposited 2021-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7W3G Structure of USP14-bound human 26S proteasome in substrate-engaged state ED2.0_USP14 Deposited 2021-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7W3H Structure of USP14-bound human 26S proteasome in substrate-engaged state ED2.1_USP14 Deposited 2021-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7W3I Structure of USP14-bound human 26S proteasome in substrate-inhibited state SB_USP14 Deposited 2021-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7W3J Structure of USP14-bound human 26S proteasome in substrate-inhibited state SC_USP14 Deposited 2021-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.50 Å
7W3K Structure of USP14-bound human 26S proteasome in substrate-inhibited state SD4_USP14 Deposited 2021-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain y 1–76（76 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7W3M Structure of USP14-bound human 26S proteasome in substrate-inhibited state SD5_USP14 Deposited 2021-11-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7XCR Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 1:1 complex Deposited 2022-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–76（76 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
7XCT Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex Deposited 2022-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain L 1–76（76 aa）
Chain N 1–76（76 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8BS9 Structure of USP36 in complex with Ubiquitin-PA Deposited 2022-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；0.3 M potassium formate, 14% (w/v) PEG 3350
Resolution 1.90 Å R-free 0.209
8BS9 Structure of USP36 in complex with Ubiquitin-PA Deposited 2022-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded ZN ZINC ION × 2 AYE prop-2-en-1-amine × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；0.3 M potassium formate, 14% (w/v) PEG 3350
Resolution 1.90 Å R-free 0.209
8C07 Structure of HECT E3 UBR5 forming K48 linked Ubiquitin chains Deposited 2022-12-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 1–76（76 aa）
Chain K 1–76（76 aa）
Not recorded SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8C61 Structure of USP54 in complex with Lys63-linked diUbiquitin-PA Deposited 2023-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–75（75 aa）
Chain C 1–76（76 aa）
Chain E 1–75（75 aa）
Chain F 1–76（76 aa）
Mutation：K63R Mutation：K63R ZN ZINC ION × 6 AYE prop-2-en-1-amine × 2 CL CHLORIDE ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；27.2 % (v/v) PEG 400, 0.1 M HEPES, 0.2 M calcium chloride
Resolution 2.50 Å R-free 0.243
8C61 Structure of USP54 in complex with Lys63-linked diUbiquitin-PA Deposited 2023-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain H 1–75（75 aa）
Chain I 1–76（76 aa）
Chain K 1–75（75 aa）
Chain L 1–76（76 aa）
Mutation：K63R Mutation：K63R ZN ZINC ION × 6 AYE prop-2-en-1-amine × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；27.2 % (v/v) PEG 400, 0.1 M HEPES, 0.2 M calcium chloride
Resolution 2.50 Å R-free 0.243
8DMQ Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester Deposited 2022-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa）
Not recorded FLC CITRATE ANION × 4 EDO 1,2-ETHANEDIOL × 2 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.19 Å R-free 0.209
8DMQ Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester Deposited 2022-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded FLC CITRATE ANION × 1 EDO 1,2-ETHANEDIOL × 1 GVE METHYL 4-AMINOBUTANOATE × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.19 Å R-free 0.209
8DMS Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester soaked with ADP-ribose Deposited 2022-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 aa）
Not recorded 1PE PENTAETHYLENE GLYCOL × 1 GVE METHYL 4-AMINOBUTANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.15 Å R-free 0.207
8DMS Crystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester soaked with ADP-ribose Deposited 2022-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 GVE METHYL 4-AMINOBUTANOATE × 1 FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium citrate, 20% w/v PEG 3350
Resolution 2.15 Å R-free 0.207
8EFW Structure of SdeA DUB Domain disulfide crosslinked with Ubiquitin Deposited 2022-09-09 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；2.8M sodium acetate: HCl pH7
Resolution 2.81 Å
8EFX Structure of OtDUB DUB Domain disulfide crosslinked with Ubiquitin Deposited 2022-09-09 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.16M Magnesium chloride, 0.08M Tris at pH 8.5, 24% PEG 8000 and 20% glycerol
Resolution 1.85 Å R-free 0.229
8EHO PRRSV-1 PLP2 domain bound to ubiquitin Deposited 2022-09-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 2 3CN 3-AMINOPROPANE × 1 NO3 NITRATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.2M Mg(NO3)2
Resolution 2.85 Å R-free 0.247
8EHO PRRSV-1 PLP2 domain bound to ubiquitin Deposited 2022-09-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 3 3CN 3-AMINOPROPANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.2M Mg(NO3)2
Resolution 2.85 Å R-free 0.247
8EHO PRRSV-1 PLP2 domain bound to ubiquitin Deposited 2022-09-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 2 3CN 3-AMINOPROPANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.2M Mg(NO3)2
Resolution 2.85 Å R-free 0.247
8F1F Structure of K48-linked tri-ubiquitin in complex with cyclic peptide Deposited 2022-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Mutation：D77 added to the C-terminus Mutation：K48R GOL GLYCEROL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Droplets were formed by mixing equal volumes of Ub3:Ub4a complex (8 mg/ml) and the crystallization solution containing 0.15 M NaCl, 23% (w/v) PEG 3350 and 0.1 M HEPES (pH 7.5)
Resolution 1.85 Å R-free 0.298
8F1F Structure of K48-linked tri-ubiquitin in complex with cyclic peptide Deposited 2022-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain a 1–76（76 aa）
Chain b 1–76（76 aa）
Chain c 1–76（76 aa）
Mutation：D77 added to the C-terminus Mutation：K48R EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Droplets were formed by mixing equal volumes of Ub3:Ub4a complex (8 mg/ml) and the crystallization solution containing 0.15 M NaCl, 23% (w/v) PEG 3350 and 0.1 M HEPES (pH 7.5)
Resolution 1.85 Å R-free 0.298
8G6G H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 5 Deposited 2023-02-15 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
8G6H H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 6 Deposited 2023-02-15 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
8G6Q H2AK119ub-modified nucleosome ubiquitin position 1 Deposited 2023-02-15 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.41 Å
8G6S H2AK119ub-modified nucleosome ubiquitin position 2 Deposited 2023-02-15 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
8GRM Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome Deposited 2022-09-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain O 1–76（76 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8H1T Cryo-EM structure of BAP1-ASXL1 bound to chromatosome Deposited 2022-10-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain M 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8IC9 Lys48-linked K48C-diubiquitin Deposited 2023-02-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：K48C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；38% 2-methyl-2,4-pentanediol and 50 mM sodium citrate (pH 4.0)
Resolution 1.25 Å R-free 0.219
8IC9 Lys48-linked K48C-diubiquitin Deposited 2023-02-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Mutation：K48C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；277 K；38% 2-methyl-2,4-pentanediol and 50 mM sodium citrate (pH 4.0)
Resolution 1.25 Å R-free 0.219
8ITP Crystal structure of USP47 catalytic domain complex with ubiquitin Deposited 2023-03-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM bis-Tris (pH 5.5), 25% PEG 3350, 50 mM MgCl2
Resolution 3.00 Å R-free 0.284
8ITP Crystal structure of USP47 catalytic domain complex with ubiquitin Deposited 2023-03-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100 mM bis-Tris (pH 5.5), 25% PEG 3350, 50 mM MgCl2
Resolution 3.00 Å R-free 0.284
8J1P Cryo-EM structure of Ufd4 in complex with K29/48 triUb Deposited 2023-04-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Chain E 1–76（76 aa）
Mutation：K29C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
8JRT Cryo-EM structure of human 26S proteasomal RP subcomplex (Ea state) bound to K11/K48-branched ubiquitin (Ub) chain composed of three Ub. Deposited 2023-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 28 PDB declaration: 28-meric
Chain u 77–152（76 aa）
Chain v 77–152（76 aa）
Chain w 77–152（76 aa）
Mutation：K63R Mutation：K63R Mutation：K63R ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；incubation time= 3 s blotting time= 2.5 s
Resolution 3.60 Å
8JTI Cryo-EM structure of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub. Deposited 2023-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 29 PDB declaration: 29-meric
Chain u 77–152（76 aa）
Chain v 77–152（76 aa）
Chain w 77–152（76 aa）
Chain x 77–152（76 aa）
Mutation：K63R Mutation：K63R Mutation：K63R Mutation：K63R ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；incubation time= 3 s blotting time= 2.5 s
Resolution 3.80 Å
8K0G Cryo-EM structure of human 26S RP (Ed state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub. Deposited 2023-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric
Chain u 77–152（76 aa）
Chain v 77–152（76 aa）
Chain w 77–152（76 aa）
Chain x 77–152（76 aa）
Mutation：K63R Mutation：K63R Mutation：K63R Mutation：K63R ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；incubation time= 3 s blotting time= 2.5 s
Resolution 3.80 Å
8K6F LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；PEG8000, Sodium Choride, Sodium HEPES
Resolution 3.41 Å R-free 0.243
8K6R LnaB-Actin-PRUb ternary complex in the presence of AMPPNP Deposited 2023-07-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；Sodium Chloride, Sodium HEPES, PEG8000
Resolution 2.76 Å R-free 0.261
8K6V LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；Magnesium acetate, MOPS, PEG8000
Resolution 2.60 Å R-free 0.307
8OYP Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic Deposited 2023-05-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded CD CADMIUM ION × 1 CL CHLORIDE ION × 1 NO3 NITRATE ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；100 mM Tris/Bicine pH 8.5, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulphate, 11.25% v/v MPD; 11.25% PEG 1000; 11.25% w/v PEG 3350 with 5 mM CdCl2
Resolution 2.44 Å R-free 0.235
8OYP Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic Deposited 2023-05-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded CD CADMIUM ION × 1 CL CHLORIDE ION × 1 NO3 NITRATE ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；100 mM Tris/Bicine pH 8.5, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulphate, 11.25% v/v MPD; 11.25% PEG 1000; 11.25% w/v PEG 3350 with 5 mM CdCl2
Resolution 2.44 Å R-free 0.235
8Q00 TssM-Ub-PA complex - A USP-like DUB from B. pseudomallei (193-430) reacted with Ub-PA Deposited 2023-07-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M ammonium citrate dibasic and 22 % w/v PEG 3350; 1:2, 1:1, 2:1 protein:reservoir ration; cryoprotected with reservoir + 25% ethylene glycol
Resolution 1.62 Å R-free 0.198
8Q00 TssM-Ub-PA complex - A USP-like DUB from B. pseudomallei (193-430) reacted with Ub-PA Deposited 2023-07-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M ammonium citrate dibasic and 22 % w/v PEG 3350; 1:2, 1:1, 2:1 protein:reservoir ration; cryoprotected with reservoir + 25% ethylene glycol
Resolution 1.62 Å R-free 0.198
8RQI Structure of Rhizobium NopD with ubiquitin Deposited 2024-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M imidazole 8.0 and 10% PEG8000
Resolution 1.94 Å R-free 0.199
8RX0 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub Deposited 2024-02-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain U 1–76（76 aa）
Not recorded 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 18–76（59 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8TXV Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Deposited 2023-08-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain M 18–76（59 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TXW Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Deposited 2023-08-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain M 18–76（59 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TXX Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Deposited 2023-08-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain M 18–76（59 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8V25 H2BK120ub-modified nucleosome ubiquitin position 1 Deposited 2023-11-21 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
8V26 H2BK120ub-modified nucleosome ubiquitin position 2 Deposited 2023-11-21 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
8V27 H2BK120ub-modified nucleosome ubiquitin position 3 Deposited 2023-11-21 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
8V28 H2BK120ub-modified nucleosome ubiquitin position 4 Deposited 2023-11-22 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
8W31 Crystal structure of parkin (R0RB):2pUb with activator compound Deposited 2024-02-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–75（75 aa） Fragment：residues 1-75
Chain C 1–75（75 aa） Fragment：residues 1-75
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 A1AE9 (S)-1-(6-benzyl-3-(4-(1,2,3,4-tetrahydroquinoline-1-carbonyl)phenyl)-6,7-dihydropyrazolo[1,5-a]pyrazin-5(4H)-yl)ethan-1-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.2 M Sodium Chloride, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350
Resolution 2.50 Å R-free 0.294
8XEP Crystal structure of a Legionella pneumophila type IV effector in complex with ubiquitin Deposited 2023-12-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；100 mM sodium acetate, pH 6.0, 160 mM ammonium sulfate, 21% PEG 4000, 20% glycerol
Resolution 2.95 Å R-free 0.228
9AVT Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin Deposited 2024-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded SO4 SULFATE ION × 4 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.2 M ammonium sulphate
Resolution 1.50 Å R-free 0.203
9AVW Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin Deposited 2024-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–152（152 aa）
Chain B 1–152（152 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 6 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；2.2 M ammonium sulphate, 20% glycerol
Resolution 1.75 Å R-free 0.222
9AZJ Structure of ubiquitinated NEMO UBAN K285C-Ub G76C bound to HOIP NZF1 Deposited 2024-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain F 1–76（76 aa）
Chain S 1–76（76 aa）
Chain Z 1–76（76 aa）
Mutation：G76C Mutation：G76C Mutation：G76C ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.6；293 K；150nl protein + 50 nl mother liquor: 0.1 M Tris/Bicine pH 8.6, 24.2% PEG 500 MME, 8% PEG 20K, 0.03 M each of NaI, NaBr, and NaF. Cryoprotected in mother liquor containing 20% glycerol
Resolution 3.32 Å R-free 0.285
9B0Z Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 2 Deposited 2024-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–152（152 aa）
Chain D 1–152（152 aa）
Chain G 1–152（152 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；20% PEG 2K MME, 0.2 M TAO and 0.1 M Tris pH 8.5. Cryoprotected in mother liquor containing 20% glycerol
Resolution 2.41 Å R-free 0.270
9B12 Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1 Deposited 2024-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–152（152 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；3:1 with reservoir solution containing 50% PEG 200 and 0.1 M HEPES pH 7.5
Resolution 1.81 Å R-free 0.269
9B12 Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1 Deposited 2024-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–152（152 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 CL CHLORIDE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；3:1 with reservoir solution containing 50% PEG 200 and 0.1 M HEPES pH 7.5
Resolution 1.81 Å R-free 0.269
9C5E Covalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin Deposited 2024-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 300 uM [U-13C; U-15N] Rcat domain from Parkin, 300 uM Ubiquitin G75-C3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 800 uM [U-13C; U-15N] Rcat domain from Parkin, 800 uM Ubiquitin G75-C3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 300 uM [U-13C; U-15N] Ubiquitin G75-C3, 300 uM Rcat domain from Parkin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 300 uM [U-13C; U-15N] Rcat domain from Parkin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 500 uM [U-13C; U-15N] Ubiquitin G75-C3, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
9D1I Structure of Ubiquitin bound to KLHDC3-EloB/C Deposited 2024-08-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；10%PEG5KMME, 0.1M HEPES pH=7.0, 5% Tascsimate pH=7.0
Resolution 2.00 Å R-free 0.189
9DBY ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome Deposited 2024-08-24 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain N 1–76（76 aa）
Mutation：G76C ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9DDE ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome Deposited 2024-08-28 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain N 1–76（76 aa）
Mutation：G76C ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9DG3 ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome Deposited 2024-09-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain N 1–76（76 aa）
Mutation：G76C ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9EBS Cryo-EM structure of USP1-UAF1-Ubiquitin in complex with TNG348 Deposited 2024-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–75（75 aa）
Not recorded A1A4Y 3-(methanesulfonyl)propan-1-amine × 1 ZN ZINC ION × 1 A1BHF 2-(4-cyclopropyl-6-methoxypyrimidin-5-yl)-9-({4-[1-methyl-4-(trifluoromethyl)-1H-imidazol-2-yl]phenyl}methyl)-7-(2,2,2-trifluoroethyl)-7,9-dihydro-8H-purin-8-imine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9EMK DupA from legionella covalently bound to ubiquitin-based probe Deposited 2024-03-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) A1H50 [(2~{R},3~{S},4~{R},5~{S})-5-[(1-ethyl-1,2,3-triazol-4-yl)methoxy]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ethanesulfonate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 6000 0.1 M HEPES pH7 0.2 M MgCl2
Resolution 2.17 Å R-free 0.239
9EMK DupA from legionella covalently bound to ubiquitin-based probe Deposited 2024-03-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) A1H50 [(2~{R},3~{S},4~{R},5~{S})-5-[(1-ethyl-1,2,3-triazol-4-yl)methoxy]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ethanesulfonate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 6000 0.1 M HEPES pH7 0.2 M MgCl2
Resolution 2.17 Å R-free 0.239
9EMK DupA from legionella covalently bound to ubiquitin-based probe Deposited 2024-03-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) A1H50 [(2~{R},3~{S},4~{R},5~{S})-5-[(1-ethyl-1,2,3-triazol-4-yl)methoxy]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ethanesulfonate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 6000 0.1 M HEPES pH7 0.2 M MgCl2
Resolution 2.17 Å R-free 0.239
9F5T Ubiquitin C-terminal clippase BpJOS Deposited 2024-04-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–152（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1 M CHES pH 9.5; 22 % PEG 8000; 1:2 protein reservoir drop ration; cryoprotected with reservoir + 20% Glycerol
Resolution 2.56 Å R-free 0.253
9F5T Ubiquitin C-terminal clippase BpJOS Deposited 2024-04-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–152（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.1 M CHES pH 9.5; 22 % PEG 8000; 1:2 protein reservoir drop ration; cryoprotected with reservoir + 20% Glycerol
Resolution 2.56 Å R-free 0.253
9F6G Human USP30 chimera bound to Ubiquitin-PA Deposited 2024-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.56 M sodium citrate pH 7.0
Resolution 1.50 Å R-free 0.211
9FN4 DUBS Parachlamydia sp. PcJOS Deposited 2024-06-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–152（152 aa）
Not recorded TLA L(+)-TARTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Molecular Dimensions Morpheus B7, 298 K.
Resolution 2.15 Å R-free 0.201
9FPA DUBS Parachlamydia sp. PcJOS orthorhombic crystal form Deposited 2024-06-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–152（152 aa）
Not recorded CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Midas G6. 35 % v/v glycerol ethoxylate, 0.2 M lithium citrate
Resolution 2.18 Å R-free 0.212
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain T 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain V 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9G7G Structure of the clippase PaJOS from Pigmentiphaga aceris Deposited 2024-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.2 M magnesium chloride, 0.1 M TRIS pH 8.5, 30 % w/v PEG4000
Resolution 1.89 Å R-free 0.231
9GKM Structure of HECT E3 TRIP12 forming K29/K48-branched Ubiquitin chains Deposited 2024-08-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–76（76 aa）
Mutation：K48R SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.69 Å
9HNW USP1-UAF1 bound to Lys63-linked diubiquitin Deposited 2024-12-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–75（75 aa）
Chain D 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K63(DAB) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
9ISZ Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation Deposited 2024-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 153–228（76 aa）
Chain D 153–228（76 aa）
Mutation：G76C Mutation：G76C SAM S-ADENOSYLMETHIONINE × 2 ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；18-20% PEG1000, 100 mM Imidazole, 200 mM CaAc2, pH 7.0
Resolution 2.60 Å R-free 0.274
9ISZ Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation Deposited 2024-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 153–228（76 aa）
Mutation：G76C SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；18-20% PEG1000, 100 mM Imidazole, 200 mM CaAc2, pH 7.0
Resolution 2.60 Å R-free 0.274
9ISZ Structure of Clr4 catalyzing K14-ubiquitinated histone H3 K9 methylation Deposited 2024-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 153–228（76 aa）
Mutation：G76C SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；18-20% PEG1000, 100 mM Imidazole, 200 mM CaAc2, pH 7.0
Resolution 2.60 Å R-free 0.274
9MC6 Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 2 Deposited 2025-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
9MC7 Cryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 4 Deposited 2025-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
9MC9 Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 1 Deposited 2025-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
9MCB Cryo-EM structure of Human UBA1-UBE2O-Ub -Recruitment state 1 Deposited 2025-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
9QHI Structure of UBA6-UbDha-BIRC6 trapped ternary complex (cluster 0) Deposited 2025-03-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–76（76 aa）
Chain E 1–76（76 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.27 Å
9QUG Structure of a UBC-Ubiquitin conjugate Deposited 2025-04-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–76（76 aa）
Not recorded GOL GLYCEROL × 4 P4K polyethylene glycol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M Trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20% (w/v) Polyethylene glycol monomethyl ether 2,000
Resolution 1.80 Å R-free 0.192
9V33 Calypso/Asx/NCP-ub complex Deposited 2025-05-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain M 77–151（75 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 5.90 Å
9V9Q Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain O 153–228（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.80 Å
9V9R Cryo-EM structure of the ncPRC1.1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain O 153–228（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å
9V9S Cryo-EM structure of the ncPRC1.1 complex bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 153–228（76 aa）
Chain O 153–228（76 aa）
Mutation：G76C Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.80 Å
9V9T Cryo-EM structure of the ncPRC1.6 complex bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 153–228（76 aa）
Chain O 153–228（76 aa）
Mutation：G76C Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.90 Å
9V9U Cryo-EM structure of the ncPRC1.4 complex containing two RNF2-BMI1 bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain O 153–228（76 aa）
Chain P 153–228（76 aa）
Mutation：G76C Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.70 Å
9V9V Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain K 153–228（76 aa）
Chain O 153–228（76 aa）
Mutation：G76C Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.80 Å
9V9W Cryo-EM structure of the ncPRC1.4 complex containing two RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 153–228（76 aa）
Chain O 153–228（76 aa）
Mutation：G76C Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
9V9Y Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 153–228（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å
9V9Z Cryo-EM structure of the ncPRC1.4 complex containing one RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain O 153–228（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain O 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain O 1–76（76 aa）
Chain U 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain O 1–76（76 aa）
Chain U 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å

278 other PDB entries and 429 assemblies. Open the comparison page and filter oligomeric states

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UniProt name UBB_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain O； PDBConstruct 1–76； UniProt 1–76

[histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D

Homo sapiens

UniProt A0A6P6IDI8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 15 DNA 2 PDB declaration: 17-meric（17） Consistent with all polymer counts Chain K； UniProt 1102–1316 Not recorded Ubiquitin × 1 （P0CG47） Retinoblastoma-binding protein 5 × 1 （Q15291） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 2-E × 2 （Q16778） DNA (145-MER) × 1 WD repeat-containing protein 5 × 1 （P61964） DNA (145-MER) × 1 Protein dpy-30 homolog × 2 （Q9C005） ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.63 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9YLE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain K 1102–1316（215 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain K 1102–1316（215 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain K 1102–1316（215 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain K 1102–1316（215 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

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UniProt name A0A6P6IDI8_PUMCO
Isoform —
PDB entities 2
Chains and sequence ranges Author chain K； PDBConstruct 11–225； UniProt 1102–1316

[histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D

Homo sapiens

UniProt O14686

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 15 DNA 2 PDB declaration: 17-meric（17） Consistent with all polymer counts Chain K； UniProt 4507–5537 Not recorded Ubiquitin × 1 （P0CG47） Retinoblastoma-binding protein 5 × 1 （Q15291） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 2-E × 2 （Q16778） DNA (145-MER) × 1 WD repeat-containing protein 5 × 1 （P61964） DNA (145-MER) × 1 Protein dpy-30 homolog × 2 （Q9C005） ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.63 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9YLE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3UVK Crystal structure of WDR5 in complex with the WDR5-interacting motif of MLL2 Deposited 2011-11-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 5337–5347（11 aa） Fragment：WDR5-interacting motif (UNP residues 5337-5347)
Not recorded BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；323 K；0.1 M ammonium sulfate, 24% PEG3350, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 323K
Resolution 1.40 Å R-free 0.192
4ERQ X-ray structure of WDR5-MLL2 Win motif peptide binary complex Deposited 2012-04-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 5333–5346（14 aa） Fragment：UNP residues 5333-5346
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.3；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.3, hanging drop, temperature 294K
Resolution 1.91 Å R-free 0.200
4ERQ X-ray structure of WDR5-MLL2 Win motif peptide binary complex Deposited 2012-04-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 5333–5346（14 aa） Fragment：UNP residues 5333-5346
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.3；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.3, hanging drop, temperature 294K
Resolution 1.91 Å R-free 0.200
4ERQ X-ray structure of WDR5-MLL2 Win motif peptide binary complex Deposited 2012-04-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 5333–5346（14 aa） Fragment：UNP residues 5333-5346
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.3；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.3, hanging drop, temperature 294K
Resolution 1.91 Å R-free 0.200
4Z4P Structure of the MLL4 SET Domain Deposited 2015-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 5385–5539（155 aa） Fragment：UNP residues 5385-5539
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；100 mM Tris-HCl 20 % Ethanol
Resolution 2.20 Å R-free 0.242
6O7G Solution structure of MLL4 PHD6 domain in complex with histone H4K16ac peptide Deposited 2019-03-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1503–1562（60 aa） Fragment：residues 1503-1562
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 2.5 mM [U-13C; U-15N] MLL4 PHD6, 7.5 mM histone H4K16ac (11-21) peptide, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
8U2Y Solution structure of the PHD6 finger of MLL4 bound to TET3 Deposited 2023-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1503–1562（60 aa）
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition 2.0 mM [U-13C; U-15N] Protein, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
9ATN NMR structure of the MLL4 PHD2/3 fingers in complex with ASXL2 Deposited 2024-02-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 227–322（96 aa）
Not recorded ZN ZINC ION × 4 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition 1.5 mM 13C, 15N MLL4 PHD2,3, 25 mM TRIS, 150 mM sodium chloride, 3 mM DTT, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain K 4507–5537（1031 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain K 4507–5537（1031 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain K 4507–5537（1031 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain K 4507–5537（1031 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å

10 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

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UniProt name KMT2D_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain K； PDBConstruct 226–1256； UniProt 4507–5537

Retinoblastoma-binding protein 5

Homo sapiens

UniProt Q15291

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 15 DNA 2 PDB declaration: 17-meric（17） Consistent with all polymer counts Chain N； UniProt 1–538 Not recorded Ubiquitin × 1 （P0CG47） [histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D × 1 （A0A6P6IDI8,O14686） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 2-E × 2 （Q16778） DNA (145-MER) × 1 WD repeat-containing protein 5 × 1 （P61964） DNA (145-MER) × 1 Protein dpy-30 homolog × 2 （Q9C005） ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.63 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9YLE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3P4F Structural and biochemical insights into MLL1 core complex assembly and regulation. Deposited 2010-10-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 371–381（11 aa） Fragment：unp residues 371-381
Mutation：Y381D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；0.2 M ammonium citrate (buffered with hydrochloric acid/sodium hydroxide to pH 7.0) and 18% PEG3350, VAPOR DIFFUSION, HANGING DROP
Resolution 2.35 Å R-free 0.249
4X8N Crystal structure of Ash2L SPRY domain in complex with phosphorylated RbBP5 Deposited 2014-12-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 347–356（10 aa） Fragment：UNP residues 347-356
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol
Resolution 2.10 Å R-free 0.277
4X8P Crystal structure of Ash2L SPRY domain in complex with RbBP5 Deposited 2014-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 344–355（12 aa） Fragment：UNP residues 344-355
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol
Resolution 2.20 Å R-free 0.271
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 330–356（27 aa） Fragment：UNP RESIDUES 330-356
Chain F 330–356（27 aa） Fragment：UNP RESIDUES 330-356
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 330–356（27 aa） Fragment：UNP RESIDUES 330-356
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 330–356（27 aa） Fragment：UNP RESIDUES 330-356
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6L The crystal structure of MLL1 (N3861I/Q3867L) in complex with RbBP5 and Ash2L Deposited 2015-12-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 330–356（27 aa） Fragment：UNP RESIDUES 330-356
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；277 K；200mM NaCl, 20% PEG 3350
Resolution 1.90 Å R-free 0.213
6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain N 1–538（538 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain N 1–538（538 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIW Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain N 1–538（538 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIX Cryo-EM structure of human MLL1-NCP complex, binding mode1 Deposited 2019-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain N 1–538（538 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6KIZ Cryo-EM structure of human MLL1-NCP complex, binding mode2 Deposited 2019-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain N 1–538（538 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6KM7 The structural basis for the internal interaction in RBBP5 Deposited 2019-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 10–325（316 aa）
Chain C 390–480（91 aa） Fragment：C-terminal distal domain
Not recorded SO4 SULFATE ION × 2 2PE NONAETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.1 M HEPES-Na, pH 7.5, 2% w/v PEG 400, 2.0 M ammonium sulfate
Resolution 1.80 Å R-free 0.194
6KM7 The structural basis for the internal interaction in RBBP5 Deposited 2019-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 10–325（316 aa）
Chain D 390–480（91 aa） Fragment：C-terminal distal domain
Not recorded SO4 SULFATE ION × 6 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.1 M HEPES-Na, pH 7.5, 2% w/v PEG 400, 2.0 M ammonium sulfate
Resolution 1.80 Å R-free 0.194
6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain A 2–538（537 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
6PWW Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome Deposited 2019-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 2–538（537 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6PWX Cryo-EM structure of RbBP5 bound to the nucleosome Deposited 2019-07-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6W5I Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class01) Deposited 2020-03-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6W5N Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Deposited 2020-03-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7BRE The crystal structure of MLL2 in complex with ASH2L and RBBP5 Deposited 2020-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 330–356（27 aa）
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Ammonium tartrate dibasic pH 7.0, 12%(w/v) Polyethylene glycol 3,350
Resolution 2.80 Å R-free 0.265
7BRE The crystal structure of MLL2 in complex with ASH2L and RBBP5 Deposited 2020-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 330–356（27 aa）
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Ammonium tartrate dibasic pH 7.0, 12%(w/v) Polyethylene glycol 3,350
Resolution 2.80 Å R-free 0.265
7MBM Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Deposited 2021-04-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.76 Å
7MBN Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Deposited 2021-04-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain N 1–538（538 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
7W67 The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 330–356（27 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.19 Å R-free 0.222
7W6A Crystal structure of the MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L complex Deposited 2021-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 330–356（27 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5 25% w/v polyethylene glycol 3350
Resolution 2.21 Å R-free 0.229
7W6I The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me1 peptide Deposited 2021-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 330–356（27 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3,350
Resolution 2.56 Å R-free 0.244
7W6J The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me2 peptide Deposited 2021-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 330–356（27 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.68 Å R-free 0.252
7W6L The crystal structure of MLL3-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 330–356（27 aa）
Chain F 330–356（27 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM sodium cacodylate, pH 6.5, 10% polyethylene glycol 3350, 0.1 M MgCl2
Resolution 2.26 Å R-free 0.223
8DU4 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Deposited 2022-07-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å

31 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RBBP5_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain N； PDBConstruct 1–538； UniProt 1–538

Set1/Ash2 histone methyltransferase complex subunit ASH2

Homo sapiens

UniProt Q9UBL3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 15 DNA 2 PDB declaration: 17-meric（17） Consistent with all polymer counts Chain T； UniProt 1–628 Not recorded Ubiquitin × 1 （P0CG47） [histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D × 1 （A0A6P6IDI8,O14686） Retinoblastoma-binding protein 5 × 1 （Q15291） Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 2-E × 2 （Q16778） DNA (145-MER) × 1 WD repeat-containing protein 5 × 1 （P61964） DNA (145-MER) × 1 Protein dpy-30 homolog × 2 （Q9C005） ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.63 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9YLE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3RSN Crystal Structure of the N-terminal region of Human Ash2L Deposited 2011-05-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 96–271（176 aa） Fragment：Ash2L N-terminal domain, UNP residues 96-271
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；100 mM Tris-HCl pH8.5, 20% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.254
3S32 Crystal structure of Ash2L N-terminal domain Deposited 2011-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 95–280（186 aa） Fragment：N-terminal domain residues 95-280
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2M MgAcetate and 17-20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.45 Å R-free 0.263
3TOJ Structure of the SPRY domain of human Ash2L Deposited 2011-09-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 370–496（127 aa） Fragment：Ash2L SPRY domain, UNP residues 370-496, 539-617
Chain A 539–617（79 aa） Fragment：Ash2L SPRY domain, UNP residues 370-496, 539-617
Chain B 370–496（127 aa） Fragment：Ash2L SPRY domain, UNP residues 370-496, 539-617
Chain B 539–617（79 aa） Fragment：Ash2L SPRY domain, UNP residues 370-496, 539-617
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；20% PEG4000, 0.15 M Li2SO4, 0.1 M Tris, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.07 Å R-free 0.206
4RIQ Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30 Interacting region (SDI) Deposited 2014-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 603–618（16 aa） Fragment：UNP residues 603-618
Chain F 603–618（16 aa） Fragment：UNP residues 603-618
Chain L 603–618（16 aa） Fragment：UNP residues 603-618
Chain X 603–618（16 aa） Fragment：UNP residues 603-618
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；323 K；0.2M MgCl2, 25% PEG 3350, 0.1M Tris pH 8.5 and 10 mM spermidine, VAPOR DIFFUSION, SITTING DROP, temperature 323K
Resolution 2.23 Å R-free 0.284
4RIQ Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30 Interacting region (SDI) Deposited 2014-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 603–618（16 aa） Fragment：UNP residues 603-618
Chain O 603–618（16 aa） Fragment：UNP residues 603-618
Chain R 603–618（16 aa） Fragment：UNP residues 603-618
Chain U 603–618（16 aa） Fragment：UNP residues 603-618
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；323 K；0.2M MgCl2, 25% PEG 3350, 0.1M Tris pH 8.5 and 10 mM spermidine, VAPOR DIFFUSION, SITTING DROP, temperature 323K
Resolution 2.23 Å R-free 0.284
4X8N Crystal structure of Ash2L SPRY domain in complex with phosphorylated RbBP5 Deposited 2014-12-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 380–495（116 aa） Fragment：UNP residues 380-495, 539-598
Chain A 539–598（60 aa） Fragment：UNP residues 380-495, 539-598
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol
Resolution 2.10 Å R-free 0.277
4X8P Crystal structure of Ash2L SPRY domain in complex with RbBP5 Deposited 2014-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 380–495（116 aa） Fragment：UNP residues 380-495, 539-598
Chain A 539–598（60 aa） Fragment：UNP residues 380-495, 539-598
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol
Resolution 2.20 Å R-free 0.271
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 380–496（117 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain A 539–598（60 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain B 380–496（117 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain B 539–598（60 aa） Fragment：UNP RESIDUES 380-496, 539-598
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 380–496（117 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain A 539–598（60 aa） Fragment：UNP RESIDUES 380-496, 539-598
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 380–496（117 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain B 539–598（60 aa） Fragment：UNP RESIDUES 380-496, 539-598
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6L The crystal structure of MLL1 (N3861I/Q3867L) in complex with RbBP5 and Ash2L Deposited 2015-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 380–496（117 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain B 539–598（60 aa） Fragment：UNP RESIDUES 380-496, 539-598
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；277 K；200mM NaCl, 20% PEG 3350
Resolution 1.90 Å R-free 0.213
6E2H Crystal structure of human Ash2L (SPRY domain and SDI motif) in complex with full length DPY-30 Deposited 2018-07-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 380–622（243 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20mM citrate pH 4.7 and polyethylene glycol (PEG) 6000
Resolution 2.24 Å R-free 0.200
6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain T 95–628（534 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain T 95–628（534 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIW Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain T 95–628（534 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIX Cryo-EM structure of human MLL1-NCP complex, binding mode1 Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain T 95–628（534 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6KIZ Cryo-EM structure of human MLL1-NCP complex, binding mode2 Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain T 95–628（534 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain D 2–534（533 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
6W5I Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class01) Deposited 2020-03-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–534（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–534（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6W5N Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Deposited 2020-03-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–534（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7BRE The crystal structure of MLL2 in complex with ASH2L and RBBP5 Deposited 2020-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 286–402（117 aa） Fragment：UNP residues 286-402 and UNP residues 445-504
Chain A 445–504（60 aa） Fragment：UNP residues 286-402 and UNP residues 445-504
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Ammonium tartrate dibasic pH 7.0, 12%(w/v) Polyethylene glycol 3,350
Resolution 2.80 Å R-free 0.265
7BRE The crystal structure of MLL2 in complex with ASH2L and RBBP5 Deposited 2020-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 286–402（117 aa） Fragment：UNP residues 286-402 and UNP residues 445-504
Chain D 445–504（60 aa） Fragment：UNP residues 286-402 and UNP residues 445-504
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Ammonium tartrate dibasic pH 7.0, 12%(w/v) Polyethylene glycol 3,350
Resolution 2.80 Å R-free 0.265
7MBM Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Deposited 2021-04-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–534（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.76 Å
7MBN Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Deposited 2021-04-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–534（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain M 95–628（534 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
7W67 The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 380–496（117 aa）
Chain A 539–598（60 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.19 Å R-free 0.222
7W6A Crystal structure of the MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L complex Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 380–496（117 aa）
Chain A 539–598（60 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5 25% w/v polyethylene glycol 3350
Resolution 2.21 Å R-free 0.229
7W6I The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me1 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 380–496（117 aa）
Chain A 539–598（60 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3,350
Resolution 2.56 Å R-free 0.244
7W6J The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me2 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 380–496（117 aa）
Chain A 539–598（60 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.68 Å R-free 0.252
7W6L The crystal structure of MLL3-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 380–496（117 aa）
Chain A 539–598（60 aa）
Chain B 380–496（117 aa）
Chain B 539–598（60 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM sodium cacodylate, pH 6.5, 10% polyethylene glycol 3350, 0.1 M MgCl2
Resolution 2.26 Å R-free 0.223
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain T 1–628（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain T 1–628（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain T 1–628（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain T 1–628（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å

31 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ASH2L_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain T； PDBConstruct 1–628； UniProt 1–628

Histone H3.1

Homo sapiens

UniProt P68431

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 15 DNA 2 PDB declaration: 17-meric（17） Consistent with all polymer counts Chain A； UniProt 2–136 Chain E； UniProt 2–136 Not recorded Ubiquitin × 1 （P0CG47） [histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D × 1 （A0A6P6IDI8,O14686） Retinoblastoma-binding protein 5 × 1 （Q15291） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 2-E × 2 （Q16778） DNA (145-MER) × 1 WD repeat-containing protein 5 × 1 （P61964） DNA (145-MER) × 1 Protein dpy-30 homolog × 2 （Q9C005） ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.63 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9YLE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2B2T Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 and phosphothreonine 3 Deposited 2005-09-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–19（19 aa） Fragment：residues 1-19
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；283 K；4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00
Resolution 2.45 Å R-free 0.266
2B2U Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 and dimethylarginine 2 Deposited 2005-09-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–15（15 aa） Fragment：residues 1-15
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；283 K；4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00
Resolution 2.95 Å R-free 0.290
2B2V Crystal structure analysis of human CHD1 chromodomains 1 and 2 bound to histone H3 resi 1-15 MeK4 Deposited 2005-09-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–15（15 aa） Fragment：residues 1-15
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；283 K；4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00
Resolution 2.65 Å R-free 0.266
2B2W Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 Deposited 2005-09-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–19（19 aa） Fragment：residues 1-19
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；283 K；4% PEG3350, 0.05M HEPES pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00
Resolution 2.40 Å R-free 0.273
2CV5 Crystal structure of human nucleosome core particle Deposited 2005-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 0–135（136 aa）
Chain E 0–135（136 aa）
Not recorded MN MANGANESE (II) ION × 9 CL CHLORIDE ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.277
2L75 Solution structure of CHD4-PHD2 in complex with H3K9me3 Deposited 2010-12-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–14（13 aa） Fragment：UNP residues 2-14
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 15；Pressure ambient
NMR sample composition 1 mM CHD4-PHD2-1; 1 mM H3K9me3-2, 20 uM DSS-3; 1 mM DTT-4; 5 mM sodium chloride-5; 10 mM sodium phosphate-6; 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] CHD4-PHD2-7; 1.1 mM H3K9me3-8; 20 uM DSS-9; 1 mM DTT-10; 5 mM sodium chloride-11; 10 mM sodium phosphate-12; 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] CHD4-PHD2-13; 1.1 mM H3K9me3-14; 20 uM DSS-15; 1 mM DTT-16; 5 mM sodium chloride-17; 10 mM sodium phosphate-18; 100% D2O | 100% D2O
Resolution not provided
2RI7 Crystal structure of PHD finger-linker-bromodomain Y17E mutant from human BPTF in the H3(1-9)K4ME2 bound state Deposited 2007-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 2–10（9 aa） Fragment：N-terminal tail residues 2-10
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 GOL GLYCEROL × 1 IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；BPTF Y17E PHD finger-linker-bromodomain (16.5 mg/ml, 20 mM Tris-HCl pH 7.5, 50 mM KCl) was pre-incubated with three-fold molar excess of H3(1-9)K4me2 peptide in the presence of 5 mM MgCl2 for about 30 min on ice. Drops were made by mixing 2 l each of the complex with the reservoir solution: 8.5% isopropanol, 0.085 M Hepes-Na, pH 7.5, 17% PEG 4000, 15% Glycerol. A 0.3 l of 1 M KCl was then added to the drops as additive., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.45 Å R-free 0.192
2UXN Structural Basis of Histone Demethylation by LSD1 Revealed by Suicide Inactivation Deposited 2007-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 2–22（21 aa） Fragment：HISTONE H3-DERIVED SUICIDE INHIBITOR, RESIDUES 2-22
Non-standard monomer：Yes (specific site not provided by mmCIF) FDA DIHYDROFLAVINE-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；PROTEIN: 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, AND 5 MM DTT RESERVOIR: 0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, AND 10 MM DTT
Resolution 2.72 Å R-free 0.272
3A1B Crystal structure of the DNMT3A ADD domain in complex with histone H3 Deposited 2009-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–21（20 aa） Fragment：ADD(ATRX-DNMT3-DNMT3L) domain(residues 476-614), UNP residues 2-21(Histone H3.1)
Not recorded ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% PEG 2000 monomethyl ether, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.29 Å R-free 0.224
3AFA The human nucleosome structure Deposited 2010-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.270
3AYW Crystal Structure of Human Nucleosome Core Particle Containing H3K56Q mutation Deposited 2011-05-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：K56Q Mutation：K56Q CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.90 Å R-free 0.273
3AZE Crystal Structure of Human Nucleosome Core Particle Containing H3K64Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：K64Q Mutation：K64Q CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.302
3AZF Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：K79Q Mutation：K79Q CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.263
3AZG Crystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：K115Q Mutation：K115Q CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.40 Å R-free 0.269
3AZH Crystal Structure of Human Nucleosome Core Particle Containing H3K122Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：K122Q Mutation：K122Q CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.49 Å R-free 0.266
3AZI Crystal Structure of Human Nucleosome Core Particle Containing H4K31Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.289
3AZJ Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.89 Å R-free 0.268
3AZK Crystal Structure of Human Nucleosome Core Particle Containing H4K59Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.20 Å R-free 0.258
3AZL Crystal Structure of Human Nucleosome Core Particle Containing H4K77Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.259
3AZM Crystal Structure of Human Nucleosome Core Particle Containing H4K79Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.89 Å R-free 0.296
3AZN Crystal Structure of Human Nucleosome Core Particle Containing H4K91Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.254
3KMT Crystal structure of vSET/SAH/H3 ternary complex Deposited 2009-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 26–33（8 aa） Fragment：residues 26-33
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.78 Å R-free 0.224
3KMT Crystal structure of vSET/SAH/H3 ternary complex Deposited 2009-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 26–33（8 aa） Fragment：residues 26-33
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.78 Å R-free 0.224
3KMT Crystal structure of vSET/SAH/H3 ternary complex Deposited 2009-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 26–33（8 aa） Fragment：residues 26-33
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.78 Å R-free 0.224
3KMT Crystal structure of vSET/SAH/H3 ternary complex Deposited 2009-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 26–33（8 aa） Fragment：residues 26-33
Chain H 26–33（8 aa） Fragment：residues 26-33
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.78 Å R-free 0.224
3KMT Crystal structure of vSET/SAH/H3 ternary complex Deposited 2009-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 26–33（8 aa） Fragment：residues 26-33
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.78 Å R-free 0.224
3KQI crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide Deposited 2009-11-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–12（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；2.0 M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.78 Å R-free 0.218
3KQI crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide Deposited 2009-11-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–12（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 GOL GLYCEROL × 2 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；2.0 M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.78 Å R-free 0.218
3LQI Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 2–10（9 aa） Fragment：Histone H3 N-terminal tail
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；293 K；0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.92 Å R-free 0.241
3LQI Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain S 2–10（9 aa） Fragment：Histone H3 N-terminal tail
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；293 K；0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.92 Å R-free 0.241
3LQI Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain T 2–10（9 aa） Fragment：Histone H3 N-terminal tail
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；293 K；0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.92 Å R-free 0.241
3LQJ Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me3 peptide Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Q 2–10（9 aa） Fragment：Histone H3 N-terminal tail
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；293 K；0.1 M Tris, 0.2 M Li2SO4, 15% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.274
3LQJ Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me3 peptide Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain T 2–10（9 aa） Fragment：Histone H3 N-terminal tail
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；293 K；0.1 M Tris, 0.2 M Li2SO4, 15% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.274
3O34 Crystal structure of TRIM24 PHD-Bromo complexed with H3(13-32)K23ac peptide Deposited 2010-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 14–33（20 aa） Fragment：UNP residues 14-35
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 BTN BIOTIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；100 mM Na-citrate (pH 5.6), 200 mM K/Na-tartrate tetrahydrate and 1.6 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.241
3O35 Crystal structure of TRIM24 PHD-Bromo complexed with H3(23-31)K27ac peptide Deposited 2010-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 24–32（9 aa） Fragment：UNP residues 14 -22
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；200 mM Na-acetate, 30% Polyethylene glycol 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.76 Å R-free 0.225
3O35 Crystal structure of TRIM24 PHD-Bromo complexed with H3(23-31)K27ac peptide Deposited 2010-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 24–32（9 aa） Fragment：UNP residues 14 -22
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；200 mM Na-acetate, 30% Polyethylene glycol 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.76 Å R-free 0.225
3O37 Crystal structure of TRIM24 PHD-Bromo complexed with H3(1-10)K4 peptide Deposited 2010-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2–11（10 aa） Fragment：UNP residues 2-11
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM Tris (pH 7.5), 30% Polyethylene glycol monomethyl ether 5000 and 100 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.254
3O37 Crystal structure of TRIM24 PHD-Bromo complexed with H3(1-10)K4 peptide Deposited 2010-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–11（10 aa） Fragment：UNP residues 2-11
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM Tris (pH 7.5), 30% Polyethylene glycol monomethyl ether 5000 and 100 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.254
3O37 Crystal structure of TRIM24 PHD-Bromo complexed with H3(1-10)K4 peptide Deposited 2010-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 2–11（10 aa） Fragment：UNP residues 2-11
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM Tris (pH 7.5), 30% Polyethylene glycol monomethyl ether 5000 and 100 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.254
3O37 Crystal structure of TRIM24 PHD-Bromo complexed with H3(1-10)K4 peptide Deposited 2010-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 2–11（10 aa） Fragment：UNP residues 2-11
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM Tris (pH 7.5), 30% Polyethylene glycol monomethyl ether 5000 and 100 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.254
3U4S Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine Deposited 2011-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 8–15（8 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NI NICKEL (II) ION × 1 ZN ZINC ION × 1 08P N-(carboxycarbonyl)-D-cysteine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG 3350, 0.1M citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.15 Å R-free 0.222
3U4S Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine Deposited 2011-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 8–15（8 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NI NICKEL (II) ION × 1 ZN ZINC ION × 1 08P N-(carboxycarbonyl)-D-cysteine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG 3350, 0.1M citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.15 Å R-free 0.222
3U5N Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-20)K9me3K14ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–21（20 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9 and acetylated K14, UNP residues 2-21
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M ammonium tartrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.95 Å R-free 0.256
3U5N Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-20)K9me3K14ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–21（20 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9 and acetylated K14, UNP residues 2-21
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M ammonium tartrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.95 Å R-free 0.256
3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 2–23（22 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.280
3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 2–23（22 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.280
3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain K 2–23（22 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.280
3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 2–23（22 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.280
3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 2–23（22 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.280
3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 2–23（22 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.280
3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain O 2–23（22 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.280
3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 2–23（22 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.280
3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 2–29（28 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.265
3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 2–29（28 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.265
3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain K 2–29（28 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.265
3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 2–29（28 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.265
3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 2–29（28 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.265
3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 2–29（28 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.265
3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain O 2–29（28 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.265
3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 2–29（28 aa） Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.265
3V43 Crystal structure of MOZ Deposited 2011-12-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Q 2–19（18 aa） Fragment：UNP RESIDUES 2-19
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.2M ammonium acetate, 0.1M tri-sodium citrate, 30% w/v PEG 4000, pH 5.6, vapor diffusion, hanging drop, temperature 293K
Resolution 1.47 Å R-free 0.176
3W96 Crystal Structure of Human Nucleosome Core Particle lacking H2A N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.296
3W97 Crystal Structure of Human Nucleosome Core Particle lacking H2B N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.20 Å R-free 0.321
3W98 Crystal Structure of Human Nucleosome Core Particle lacking H3.1 N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 29–136（108 aa） Fragment：UNP residues 29-136
Chain E 29–136（108 aa） Fragment：UNP residues 29-136
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.42 Å R-free 0.303
3W99 Crystal Structure of Human Nucleosome Core Particle lacking H4 N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.312
3WA9 The nucleosome containing human H2A.Z.1 Deposited 2013-04-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.07 Å R-free 0.271
3WAA The nucleosome containing human H2A.Z.2 Deposited 2013-04-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.271
3WKJ The nucleosome containing human TSH2B Deposited 2013-10-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.291
3X1S Crystal structure of the nucleosome core particle Deposited 2014-11-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70mM KCL, 70-90mM MnCl2, 24% MPD, 20mM Na-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.81 Å R-free 0.270
3X1T Crystal structure of nucleosome core particle consisting of mouse testis specific histone variants H2aa and H2ba Deposited 2014-11-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MN MANGANESE (II) ION × 22 CL CHLORIDE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70mM Kcl, 70-90mM MnCl2, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.81 Å R-free 0.266
3X1U Crystal structure of nucleosome core particle in the presence of histone variants involved in reprogramming Deposited 2014-11-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MN MANGANESE (II) ION × 4 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70 mM KCl, 70-90 mM MnCl2, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.25 Å R-free 0.270
3X1V Crystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming Deposited 2014-11-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MN MANGANESE (II) ION × 19 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70 mM KCl, 70-90 mM MnCl2, Na-cocodylate, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.92 Å R-free 0.259
3ZVY PHD finger of human UHRF1 in complex with unmodified histone H3 N- terminal tail Deposited 2011-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–9（8 aa） Fragment：RESIDUES 2-9
Not recorded ZN ZINC ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；290 K；CRYSTALS WERE OBTAINED AT 17 DEGREES USING THE VAPOR DIFFUSION METHOD BY MIXING A PROTEIN SOLUTION AT A CONCENTRATION OF 606 MICROM (IN 20 MM TRIS PH 7, 150 MM NACL, 0.5 MM TCEP, 25 MICROM ZNCL2 AND 0.1 MM PMSF) AND 10-FOLD EXCESS OF PEPTIDE WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (0.1 M TRIS PH 8.5, 0.2 M MGCL2, 30 % PEG 4000). CRYSTALS WERE CRYOPROTECTED WITH 15 % MPD AND FLASH FROZEN IN LIQUID NITROGEN.
Resolution 1.95 Å R-free 0.227
3ZVY PHD finger of human UHRF1 in complex with unmodified histone H3 N- terminal tail Deposited 2011-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–9（8 aa） Fragment：RESIDUES 2-9
Not recorded ZN ZINC ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；290 K；CRYSTALS WERE OBTAINED AT 17 DEGREES USING THE VAPOR DIFFUSION METHOD BY MIXING A PROTEIN SOLUTION AT A CONCENTRATION OF 606 MICROM (IN 20 MM TRIS PH 7, 150 MM NACL, 0.5 MM TCEP, 25 MICROM ZNCL2 AND 0.1 MM PMSF) AND 10-FOLD EXCESS OF PEPTIDE WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (0.1 M TRIS PH 8.5, 0.2 M MGCL2, 30 % PEG 4000). CRYSTALS WERE CRYOPROTECTED WITH 15 % MPD AND FLASH FROZEN IN LIQUID NITROGEN.
Resolution 1.95 Å R-free 0.227
4BD3 Phf19 links methylated lysine 36 of histone H3 to regulation of Polycomb activity Deposited 2012-10-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 32–42（11 aa） Fragment：H3(31-41)K36ME3, RESIDUES 32-42
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure 1.0
NMR sample composition 90% WATER/10% D2O
Resolution not provided
4C1Q Crystal structure of the PRDM9 SET domain in complex with H3K4me2 and AdoHcy. Deposited 2013-08-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–11（10 aa） Fragment：N-TERMINUS, RESIDUES 2-11
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；278 K；0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 5.5 AND 25% W/V PEG3350
Resolution 2.30 Å R-free 0.252
4F4U The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5 Deposited 2012-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 5–16（12 aa） Fragment：UNP residue 5-16
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；16% PEG 4000, 6% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.261
4F4U The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5 Deposited 2012-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 5–16（12 aa） Fragment：UNP residue 5-16
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；16% PEG 4000, 6% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.261
4F56 The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5 Deposited 2012-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 5–16（12 aa） Fragment：UNP residue 5-16
Not recorded ZN ZINC ION × 1 CGK 3-[(2R,3aR,5R,6R,6aR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-2,6-dihydroxytetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]propanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% PEG 10000, 0.1M Tris, pH 8.5, vapor diffusion, hanging drop, temperature 298K
Resolution 1.70 Å R-free 0.233
4F56 The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5 Deposited 2012-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 5–16（12 aa） Fragment：UNP residue 5-16
Not recorded ZN ZINC ION × 1 CGK 3-[(2R,3aR,5R,6R,6aR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-2,6-dihydroxytetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]propanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% PEG 10000, 0.1M Tris, pH 8.5, vapor diffusion, hanging drop, temperature 298K
Resolution 1.70 Å R-free 0.233
4FT2 crystal structure of Zea mays ZMET2 in complex H3(1-15)K9me2 peptide and SAH Deposited 2012-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 16–30（15 aa） Fragment：histone H3 peptide, UNP residues 16-30
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.2 M calcium acetate, 0.1 M imidazole pH 8.0, and 10% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.20 Å R-free 0.277
4FT4 crystal structure of Zea mays ZMET2 in complex H3(1-32)K9me2 peptide and SAH Deposited 2012-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Q 33–64（32 aa） Fragment：histone H3 peptide, UNP residues 33-64
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M sodium citrate, 0.1 M bis-tris propane, pH 6.5 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.248
4FT4 crystal structure of Zea mays ZMET2 in complex H3(1-32)K9me2 peptide and SAH Deposited 2012-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 33–64（32 aa） Fragment：histone H3 peptide, UNP residues 33-64
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M sodium citrate, 0.1 M bis-tris propane, pH 6.5 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.248
4FWF Complex structure of LSD2/AOF1/KDM1b with H3K4 mimic Deposited 2012-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2–21（20 aa） Fragment：UNP residues 2-21
Mutation：K4M ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；21% PEG3350, 200mM diammonium citrate, pH 7, VAPOR DIFFUSION, temperature 298K
Resolution 2.70 Å R-free 0.237
4LK9 Crystal Structure of MOZ double PHD finger histone H3 tail complex Deposited 2013-07-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–22（21 aa） Fragment：unp residues 2-22
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；283 K；100 mM Na-Hepes, 1.4 M sodium citrate, pH 7.5, VAPOR DIFFUSION, temperature 283K
Resolution 1.60 Å R-free 0.186
4LKA Crystal Structure of MOZ double PHD finger histone H3K9ac complex Deposited 2013-07-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–22（21 aa） Fragment：unp residues 2-22
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；283 K；100 mM Na-Hepes, 1.4 M sodium citrate, pH 7.5, vapor diffusion, temperature 283K
Resolution 1.61 Å R-free 0.185
4LLB Crystal Structure of MOZ double PHD finger histone H3K14ac complex Deposited 2013-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–22（21 aa） Fragment：unp residues 2-22
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；283 K；100 mM Tris-Cl, 200 mM Li2SO4, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, temperature 283K
Resolution 2.50 Å R-free 0.266
4LLB Crystal Structure of MOZ double PHD finger histone H3K14ac complex Deposited 2013-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–22（21 aa） Fragment：unp residues 2-22
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；283 K；100 mM Tris-Cl, 200 mM Li2SO4, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, temperature 283K
Resolution 2.50 Å R-free 0.266
4N4H Crystal structure of the Bromo-PWWP of the mouse zinc finger MYND-type containing 11 isoform alpha in complex with histone H3.1K36me3 Deposited 2013-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–43（22 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；289 K；25% (w/v) polyethylene glycol 4000, 0.1M Tris-HCl, pH 8.3, 0.2M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.30 Å R-free 0.263
4UP0 Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and a H3K4me2 peptide Deposited 2014-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–16（15 aa） Fragment：RESIDUES 2-16
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 1 M SODIUM CITRATE, 0.1 M TRIS PH 7, 0.2 M NACL
Resolution 1.28 Å R-free 0.166
4YM5 Crystal structure of the human nucleosome containing 6-4PP (inside) Deposited 2015-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 4.00 Å R-free 0.289
4YM6 Crystal structure of the human nucleosome containing 6-4PP (outside) Deposited 2015-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.51 Å R-free 0.287
4Z0R Crystal Structure of the CW domain of ZCWPW2 mutant F78R in complex with histone H3 peptide Deposited 2015-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–16（15 aa） Fragment：N-terminal tail (UNP residues 2-16)
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 UNX UNKNOWN LIGAND × 9 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2 M ammonium sulfate, 2% PEG400, 0.1 M HEPES sodium
Resolution 1.75 Å R-free 0.192
4Z2M Crystal structure of human SPT16 Mid-AID/H3-H4 tetramer FACT Histone complex Deposited 2015-03-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain G 35–136（102 aa） Fragment：UNP residues 35-136
Chain I 35–136（102 aa） Fragment：UNP residues 35-136
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；10% PEG400, 0.9-1.1 M Imidazole, 100-150 mM L-histidine
Resolution 2.98 Å R-free 0.246
5AV5 human nucleosome core particle Deposited 2015-06-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions LIQUID DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.233
5AV6 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.229
5AV8 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.233
5AV9 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.239
5AVB human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.236
5AVC human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.238
5B24 The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer Deposited 2015-12-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.60 Å R-free 0.249
5B2I Human nucleosome containing CpG unmethylated DNA Deposited 2016-01-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 3.00 Å R-free 0.257
5B2J Human nucleosome containing CpG methylated DNA Deposited 2016-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.60 Å R-free 0.252
5B31 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1. Deposited 2016-02-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.20 Å R-free 0.271
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain N 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain V 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5CPI Nucleosome containing unmethylated Sat2R DNA Deposited 2015-07-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.90 Å R-free 0.295
5CPJ Nucleosome containing methylated Sat2R DNA Deposited 2015-07-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.15 Å R-free 0.295
5CPK Nucleosome containing methylated Sat2L DNA Deposited 2015-07-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.63 Å R-free 0.284
5GSE Crystal structure of unusual nucleosome Deposited 2016-08-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；potassium bromide, potassium thiocyanate, Tris-HCl, PGA-LM, PEG 400
Resolution 3.14 Å R-free 0.255
5GSU Crystal structure of nucleosome core particle consisting of human testis-specific histone variants, Th2A and Th2B Deposited 2016-08-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20mM Pottasium Cacodylate pH 6.0, 60-70mM KCl, 70-90mM MnCl2
Resolution 3.10 Å R-free 0.257
5GT0 Crystal structure of nucleosome complex with human testis-specific histone variants, Th2a Deposited 2016-08-18 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MN MANGANESE (II) ION × 14 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；60-70mM KCl, 70-90mM MnCl2, 24% MPD
Resolution 2.82 Å R-free 0.280
5GT3 Crystal structure of nucleosome particle in the presence of human testis-specific histone variant, hTh2b Deposited 2016-08-18 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MN MANGANESE (II) ION × 12 CL CHLORIDE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；60-70mM KCl, 70-90mM MnCl2, 24% MPD
Resolution 2.91 Å R-free 0.258
5GTC Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle Deposited 2016-08-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.70 Å R-free 0.267
5HJB AF9 YEATS in complex with histone H3 Crotonylation at K9 Deposited 2016-01-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 4–11（8 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；20% (w/v) polyethylene glycol 4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 3% MPD
Resolution 2.70 Å R-free 0.253
5HJC BRD3 second bromodomain in complex with histone H3 acetylation at K18 Deposited 2016-01-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 16–24（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30%(w/v) polyethylene glycol methyl ether 5000, 0.2 M ammonium sulfate, 0.1 M MES, 0.1 M guanidine hydrochloride
Resolution 2.60 Å R-free 0.269
5HJD AF9 YEATS in complex with histone H3 Crotonylation at K18 Deposited 2016-01-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 15–21（7 aa）
Chain D 15–21（7 aa）
Chain F 15–21（7 aa）
Chain L 15–21（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 3 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；20%(w/v) polyethylene glycol 4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.1 M copper chloride dihydrate
Resolution 2.81 Å R-free 0.273
5HJD AF9 YEATS in complex with histone H3 Crotonylation at K18 Deposited 2016-01-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain H 15–21（7 aa）
Chain I 15–21（7 aa）
Chain J 15–21（7 aa）
Chain M 15–21（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；20%(w/v) polyethylene glycol 4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.1 M copper chloride dihydrate
Resolution 2.81 Å R-free 0.273
5IQL Crystal structure of YEATS2 YEATS bound to H3K27cr peptide Deposited 2016-03-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 25–32（8 aa） Fragment：H3 peptide (UNP RESIDUES 25-32)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；0.1M Bis-Tris propane, 4.0 M NH4Ac, pH 7.0
Resolution 2.10 Å R-free 0.253
5J9S ENL YEATS in complex with histone H3 acetylation at K27 Deposited 2016-04-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 16–40（25 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M K/Na Tartrate, 0.1M Sodium citrate tribasic dihydrate, pH 5.6, 2M (NH4)2SO4
Resolution 2.70 Å R-free 0.210
5JRG Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF) Deposited 2016-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.50 Å R-free 0.245
5KKL Structure of ctPRC2 in complex with H3K27me3 and H3K27M Deposited 2016-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 23–31（9 aa）
Mutation：K2027M ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；15% PEG4000, 175mM ammonium citrate, pH 7.0
Resolution 2.94 Å R-free 0.234
5T1G chromo shadow domain of CBX1 in complex with a histone peptide Deposited 2016-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 39–53（15 aa） Fragment：unp residues 39-53
Non-standard monomer：Yes (specific site not provided by mmCIF) UNX UNKNOWN LIGAND × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.5 M sodium citrate, 0.1 M HEPES
Resolution 1.90 Å R-free 0.243
5T1I CBX3 chromo shadow domain in complex with histone H3 peptide Deposited 2016-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 39–53（15 aa） Fragment：unp residues 39-53
Non-standard monomer：Yes (specific site not provided by mmCIF) UNX UNKNOWN LIGAND × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG 3350, 0.2 M sodium chloride, 0.1 M Hepes, 5% Ethylene Glycol
Resolution 1.60 Å R-free 0.239
5T8R Crystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer Deposited 2016-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 2–11（10 aa） Fragment：UNP residues 2-11
Not recorded ZN ZINC ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2.2 M Na/K phosphate
Resolution 2.40 Å R-free 0.235
5T8R Crystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer Deposited 2016-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2–11（10 aa） Fragment：UNP residues 2-11
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2.2 M Na/K phosphate
Resolution 2.40 Å R-free 0.235
5T8R Crystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer Deposited 2016-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 2–11（10 aa） Fragment：UNP residues 2-11
Not recorded ZN ZINC ION × 4 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2.2 M Na/K phosphate
Resolution 2.40 Å R-free 0.235
5T8R Crystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer Deposited 2016-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 2–11（10 aa） Fragment：UNP residues 2-11
Not recorded ZN ZINC ION × 4 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2.2 M Na/K phosphate
Resolution 2.40 Å R-free 0.235
5TBN Solution NMR structure of PHF20 PHD domain in complex with a histone H3K4me2 peptide Deposited 2016-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–12（11 aa） Fragment：residues 2-12
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate；Pressure 101325
NMR sample composition 1.5 mM [U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.5 mM [U-13C; U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 2 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5VA6 CRYSTAL STRUCTURE OF ATXR5 IN COMPLEX WITH HISTONE H3.1 MONO-METHYLATED ON R26 Deposited 2017-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 20–37（18 aa） Fragment：residues 20-37
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；50% polypropylene glycol 400, 5% DMSO, 0.1 M HEPES-NaOH (pH 6.0)
Resolution 2.40 Å R-free 0.297
5VA6 CRYSTAL STRUCTURE OF ATXR5 IN COMPLEX WITH HISTONE H3.1 MONO-METHYLATED ON R26 Deposited 2017-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 20–37（18 aa） Fragment：residues 20-37
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；50% polypropylene glycol 400, 5% DMSO, 0.1 M HEPES-NaOH (pH 6.0)
Resolution 2.40 Å R-free 0.297
5WFC Humanized mutant of the Chaetomium thermophilum Polycomb Repressive Complex 2 bound to the inhibitor GSK343 Deposited 2017-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 23–33（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 A97 N-[(6-methyl-2-oxo-4-propyl-1,2-dihydropyridin-3-yl)methyl]-6-[2-(4-methylpiperazin-1-yl)pyridin-4-yl]-1-(propan-2-yl)-1H-indazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM sodium malonate pH 7.0, 16% PEG 3350, 43 mM 3-cyclohexyl-1-propylphosphocholine
Resolution 2.28 Å R-free 0.203
5WVO Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3 Deposited 2016-12-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 2–37（36 aa） Fragment：UNP residues 2-37
Mutation：K18C,K23C ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；100mM Bis-Tris (pH 6.0), 200mM lithium sulfate monohydrate, 20% PEG 10000
Resolution 2.00 Å R-free 0.239
5XF3 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RRK (1R,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
Resolution 2.60 Å R-free 0.270
5XF4 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (S,S-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 SSK (1S,2S)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
Resolution 2.87 Å R-free 0.266
5XF5 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,S-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RSK (1S,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55mM MnCl2, 25-49mM KCl, 20mM K-Cacodylate pH 6.0
Resolution 2.82 Å R-free 0.264
5XFR Ternary complex of MTF2, DNA and histone Deposited 2017-04-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain C 34–41（8 aa）
Chain D 34–41（8 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M MES monohydrate-pH 6.5, 0.2M ammonium sulfate, 25% PEG monomethyl ether 5000, 10% glycerol
Resolution 2.25 Å R-free 0.231
5Y0C Crystal Structure of the human nucleosome at 2.09 angstrom resolution Deposited 2017-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 10 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.09 Å R-free 0.249
5Y0D Crystal Structure of the human nucleosome containing the H2B E76K mutant Deposited 2017-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 1.99 Å R-free 0.252
5Z23 Crystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD Deposited 2017-12-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–75（75 aa）
Chain A 114–136（23 aa）
Chain E 1–75（75 aa）
Chain E 114–136（23 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.73 Å R-free 0.261
5Z30 The crystal structure of the nucleosome containing a cancer-associated histone H2A.Z R80C mutant Deposited 2018-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.45 Å R-free 0.243
5ZBX The crystal structure of the nucleosome containing histone H3.1 CATD(V76Q, K77D) Deposited 2018-02-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–75（75 aa）
Chain A 114–136（23 aa）
Chain E 1–75（75 aa）
Chain E 114–136（23 aa）
Mutation：V76Q, K77D Mutation：V76Q, K77D Mutation：V76Q, K77D Mutation：V76Q, K77D CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.58 Å R-free 0.249
6BHD Crystal structure of SETDB1 with a modified H3 peptide Deposited 2017-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 5–20（16 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) UNX UNKNOWN LIGAND × 35 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% glycerol
Resolution 1.25 Å R-free 0.183
6BHE Crystal structure of SETDB1 with a modified H3 peptide Deposited 2017-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 5–20（16 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) UNX UNKNOWN LIGAND × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% glycerol
Resolution 1.35 Å R-free 0.172
6BHG Crystal structure of SETDB1 with a modified H3 peptide Deposited 2017-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 5–20（16 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) UNX UNKNOWN LIGAND × 40 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；20% PEG5000 MME, 0.1 M Bis-Tris
Resolution 1.45 Å R-free 0.176
6BHH Crystal structure of SETDB1 with a modified H3 peptide Deposited 2017-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 5–20（16 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 UNX UNKNOWN LIGAND × 26 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；25% PEG3350, 0.2 M lithium sulfate, 0.1 M HEPES
Resolution 1.85 Å R-free 0.237
6BHI Crystal structure of SETDB1 with a modified H3 peptide Deposited 2017-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 5–20（16 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) UNX UNKNOWN LIGAND × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；25% PEG3350, 0.2 M lithium sulfate, 0.1 M HEPES
Resolution 1.40 Å R-free 0.187
6D07 Crystal structure of the complex between human chromobox homolog 1 (CBX1) and H3K9me3 peptide Deposited 2018-04-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–16（15 aa） Fragment：H3K9(me)3 peptide (UNP residues 2-16)
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M sodium chloride, 0.1 M Tris, pH 8.0, 30% w/v PEG3350
Resolution 2.10 Å R-free 0.257
6D07 Crystal structure of the complex between human chromobox homolog 1 (CBX1) and H3K9me3 peptide Deposited 2018-04-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–16（15 aa） Fragment：H3K9(me)3 peptide (UNP residues 2-16)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M sodium chloride, 0.1 M Tris, pH 8.0, 30% w/v PEG3350
Resolution 2.10 Å R-free 0.257
6D08 Crystal structure of an engineered bump-hole complex of mutant human chromobox homolog 1 (CBX1) with H3K9bn peptide Deposited 2018-04-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–16（15 aa） Fragment：H3K9bn peptide (UNP residues 2-16)
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M citrate, pH 5.0, 3 M ammonium sulfate
Resolution 2.10 Å R-free 0.252
6D08 Crystal structure of an engineered bump-hole complex of mutant human chromobox homolog 1 (CBX1) with H3K9bn peptide Deposited 2018-04-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–16（15 aa） Fragment：H3K9bn peptide (UNP residues 2-16)
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M citrate, pH 5.0, 3 M ammonium sulfate
Resolution 2.10 Å R-free 0.252
6HKT Structure of an H1-bound 6-nucleosome array Deposited 2018-09-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 48 PDB declaration: 50-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain U 1–136（136 aa）
Chain Y 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Chain k 1–136（136 aa）
Chain o 1–136（136 aa）
Chain u 1–136（136 aa）
Chain y 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293.15 K；15% MPD, 0.1 M NaCl and 0.1 M Tris pH 8.8
Resolution 9.70 Å R-free 0.286
6HTS Cryo-EM structure of the human INO80 complex bound to nucleosome Deposited 2018-10-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain I 1–136（136 aa）
Chain M 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6IPU Human nucleosome core particle containing 145 bp of DNA Deposited 2018-11-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 39–136（98 aa）
Chain E 39–136（98 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 1.99 Å R-free 0.263
6IQ4 Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups. Deposited 2018-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 39–136（98 aa）
Chain E 39–136（98 aa）
Not recorded AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 4 D0X [Ru(eta(6)-p-cymene)Cl-2(pta) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.25 Å R-free 0.257
6JOU Crystal structure of the human nucleosome containing H2A.Z.1 S42R Deposited 2019-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.17 Å R-free 0.250
6JR0 Crystal structure of the human nucleosome phased with 12 selenium atoms Deposited 2019-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.50 Å R-free 0.253
6JR1 Crystal structure of the human nucleosome phased with 16 selenium atoms Deposited 2019-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.40 Å R-free 0.243
6JXD Human nucleosome core particle with cohesive end DNA termini Deposited 2019-04-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 39–136（98 aa）
Chain E 39–135（97 aa）
Not recorded MN MANGANESE (II) ION × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.25 Å R-free 0.292
6K1I Human nucleosome core particle with gammaH2A.X variant Deposited 2019-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 23 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；potassium chloride, manganese chloride, potassium cacodylate
Resolution 2.75 Å R-free 0.277
6K1J Human nucleosome core particle with H2A.X variant Deposited 2019-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Potassium Chloride, Manganese Chloride, Potassium Cacodylate
Resolution 2.85 Å R-free 0.319
6K1K Human nucleosome core particle with H2A.X S139E variant Deposited 2019-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 33 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；potassium chloride, manganese chloride, potassium cacodylate
Resolution 2.20 Å R-free 0.275
6KE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 41–136（96 aa）
Chain E 41–136（96 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.22 Å R-free 0.230
6KVD Crystal structure of human nucleosome containing H2A.J Deposited 2019-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 13 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.21 Å R-free 0.257
6L49 H3-CA-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain S 1–136（136 aa）
Chain W 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 18.90 Å
6L4A H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain S 1–136（136 aa）
Chain W 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 12.30 Å
6L9H The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 41–136（96 aa）
Chain E 41–136（96 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.278
6L9Z 338 bp di-nucleosome assembled with linker histone H1.X Deposited 2019-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded CL CHLORIDE ION × 8 CA CALCIUM ION × 65 K POTASSIUM ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate
Resolution 2.50 Å R-free 0.256
6LA2 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 38-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain U 1–136（136 aa）
Chain Y 1–136（136 aa）
Chain e 1–136（136 aa）
Chain i 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, Potassium chloride, Sodium acetate
Resolution 3.89 Å R-free 0.267
6LA8 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded CA CALCIUM ION × 23 K POTASSIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate (cryo-25% MPD)
Resolution 3.40 Å R-free 0.265
6LA9 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 (high cryoprotectant) Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded CA CALCIUM ION × 40 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.70 Å R-free 0.266
6LAB 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0 Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded CA CALCIUM ION × 20 K POTASSIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.20 Å R-free 0.262
6LE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 41–136（96 aa）
Chain E 41–136（96 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.281
6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CA CALCIUM ION × 6 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.00 Å R-free 0.261
6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded CA CALCIUM ION × 8 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.00 Å R-free 0.261
6M3V 355 bp di-nucleosome harboring cohesive DNA termini Deposited 2020-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded K POTASSIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
Resolution 4.60 Å R-free 0.261
6M44 355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant) Deposited 2020-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
Resolution 3.81 Å R-free 0.286
6M4D Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6M4G Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6M4H Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6R8Y Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6R8Z Cryo-EM structure of NCP_THF2(-1)-UV-DDB Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6R90 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6R91 Cryo-EM structure of NCP_THF2(-3)-UV-DDB Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6R92 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6R93 Cryo-EM structure of NCP-6-4PP Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6R94 Cryo-EM structure of NCP_THF2(-3) Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6T90 OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2019-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–134（134 aa）
Not recorded PTD PENTANEDIAL × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
6T93 Nucleosome with OCT4-SOX2 motif at SHL-6 Deposited 2019-10-25 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.49 Å
6UPK Structure of FACT_subnucleosome complex 1 Deposited 2019-10-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
6UPL Structure of FACT_subnucleosome complex 2 Deposited 2019-10-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.40 Å
6USJ Structure of two nucleosomes bridged by human PARP2 Deposited 2019-10-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Buffer was pH-adjusted and filtered through a 0.22 um filter.
cryo-EM vitrification conditions Cryogen ETHANE；Blot time 2s, blot force 0
Resolution 10.50 Å
6V2K The nucleosome structure after H2A-H2B exchange Deposited 2019-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.60 Å R-free 0.248
6V41 crystal structure of CDY1 chromodomain bound to H3K9me3 Deposited 2019-11-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain QQQ 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) UNX UNKNOWN LIGAND × 20 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；1.4 M sodium citrate, 0.1 M HEPES
Resolution 1.60 Å R-free 0.215
6V92 RSC-NCP Deposited 2019-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 33 PDB declaration: 35-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 32–43（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
Resolution 1.70 Å R-free 0.241
6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 32–43（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) UNX UNKNOWN LIGAND × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
Resolution 1.70 Å R-free 0.241
6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 32–43（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) UNX UNKNOWN LIGAND × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
Resolution 1.70 Å R-free 0.241
6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 32–43（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) UNX UNKNOWN LIGAND × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
Resolution 1.70 Å R-free 0.241
6WW4 Crystal structure of HERC2 ZZ domain in complex with histone H3 tail Deposited 2020-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–7（6 aa） Fragment：fusion protein
Not recorded ZN ZINC ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 17% PEG 10000
Resolution 2.25 Å R-free 0.243
6WW4 Crystal structure of HERC2 ZZ domain in complex with histone H3 tail Deposited 2020-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–7（6 aa） Fragment：fusion protein
Not recorded ZN ZINC ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 17% PEG 10000
Resolution 2.25 Å R-free 0.243
6YIH Structure of Chromosomal Passenger Complex (CPC) bound to phosphorylated Histone 3 peptide at 2.6 A. Deposited 2020-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 2–13（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；291 K；20 % (w/v) PEG 4,000, 100 mM HEPES pH 7.0, 150 mM ammonium sulphate
Resolution 2.55 Å R-free 0.259
6YOV OCT4-SOX2-bound nucleosome - SHL+6 Deposited 2020-04-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–134（134 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
7BWD Structure of Dot1L-H2BK34ub Nucleosome Complex Deposited 2020-04-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.32 Å
7C0M Human cGAS-nucleosome complex Deposited 2020-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain a 2–136（135 aa）
Chain e 2–136（135 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7CCQ Structure of the 1:1 cGAS-nucleosome complex Deposited 2020-06-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 39–136（98 aa）
Chain E 39–136（98 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7CCR Structure of the 2:2 cGAS-nucleosome complex Deposited 2020-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain A 39–136（98 aa）
Chain E 39–136（98 aa）
Chain L 39–136（98 aa）
Chain P 39–136（98 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
7COW 353 bp di-nucleosome harboring cohesive DNA termini with linker histone H1.0 Deposited 2020-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded CA CALCIUM ION × 3 K POTASSIUM ION × 5 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；potassium acetate, calcium chloride, potassium chloride
Resolution 2.86 Å R-free 0.297
7D1Z Cryo-EM structure of SET8-nucleosome complex Deposited 2020-09-15 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7DBP Linker histone defines structure and self-association behaviour of the 177 bp human chromosome Deposited 2020-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7E8D NSD2 E1099K mutant bound to nucleosome Deposited 2021-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 3 SFG SINEFUNGIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7K5X Cryo-EM structure of a chromatosome containing human linker histone H1.0 Deposited 2020-09-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
7K5Y Cryo-EM structure of a chromatosome containing human linker histone H1.4 Deposited 2020-09-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7K60 Cryo-EM structure of a chromatosome containing human linker histone H1.10 Deposited 2020-09-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7K61 Cryo-EM structure of 197bp nucleosome aided by scFv Deposited 2020-09-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
7K63 Cryo-EM structure of a chromatosome containing chimeric linker histone gH1.10-ncH1.4 Deposited 2020-09-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
7KLR Solution structure of the PHD1 domain of histone demethylase KDM5A in complex with a histone H3(1-10) peptide Deposited 2020-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–11（10 aa）
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition 900 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 4000 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 550 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 800 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1250 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 400 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
7LBK Crystal structure of human Survivin bound to histone H3 T3phK4me3 peptide Deposited 2021-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 2–13（12 aa）
Chain D 2–13（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；The crystal was obtained by mixing 1 uL of protein at 10 mg/mL with 1 uL of mother liquor composed of 0.16 M potassium/sodium tartrate, 14% PEG 3350.
Resolution 2.70 Å R-free 0.253
7LBO Crystal structure of human Survivin bound to histone H3 T3phK4me1 peptide Deposited 2021-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 2–13（12 aa）
Chain F 2–13（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；1 uL of protein at 10 mg/mL was mixed with 1 uL of buffer composed of 0.16 M potassium/sodium tartrate, 12% PEG 3350
Resolution 2.50 Å R-free 0.261
7LBP Crystal structure of human Survivin bound to histone H3T3phK4ac peptide Deposited 2021-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–13（12 aa）
Chain D 2–13（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；1 uL of protein at 10mg/mL was mixed with 1 uL of buffer composed of 0.16 M potassium/sodium tartrate, 12% PEG 3350
Resolution 2.60 Å R-free 0.247
7LBQ Crystal structure of human Survivin bound to histone H3 T3phK4me2 peptide Deposited 2021-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 2–13（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；1 uL of protein was mixed with 1uL of buffer composed of 2.25 mM spermine, 9 mM MgCl2, 0.9 mM spermidine, 1.8 mM cobalt (III)hexamine chloride, 0.05 sodium cacodylate pH 7.0, 5% PEG 400
Resolution 2.69 Å R-free 0.268
7LYA Cryo-EM structure of the human nucleosome core particle with linked histone proteins H2A and H2B Deposited 2021-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
7LYB Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Deposited 2021-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
7LYC Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Deposited 2021-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
7MJU Crystal structure of human AF10 PZP bound to histone H3 tail Deposited 2021-04-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–14（13 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.09 M Tris, 22.5% PEG 3350, and 10 mM spermine tetrahydrochloride
Resolution 2.10 Å R-free 0.206
7NL0 Cryo-EM structure of the Lin28B nucleosome core particle Deposited 2021-02-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7SCY Nuc147 bound to single BRCT Deposited 2021-09-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7SCZ Nuc147 bound to multiple BRCTs Deposited 2021-09-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7U0G structure of LIN28b nucleosome bound 3 OCT4 Deposited 2022-02-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
7U0I Structure of LIN28b nucleosome bound 2 OCT4 Deposited 2022-02-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
7U0J Structure of 162bp LIN28b nucleosome Deposited 2022-02-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7V6Q Crystal structure of sNASP-ASF1A-H3.1-H4 complex Deposited 2021-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–136（136 aa）
Not recorded GOL GLYCEROL × 4 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；18% (v/v) Tacsimate, pH 5.0 11% (v/v) PEG2000MME
Resolution 3.00 Å R-free 0.203
7V6Q Crystal structure of sNASP-ASF1A-H3.1-H4 complex Deposited 2021-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 1–136（136 aa）
Not recorded GOL GLYCEROL × 2 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；18% (v/v) Tacsimate, pH 5.0 11% (v/v) PEG2000MME
Resolution 3.00 Å R-free 0.203
7V90 Telomeric mononucleosome Deposited 2021-08-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7V96 Telomeric Dinucleosome Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
7V9C Telomeric Dinucleosome in open state Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7V9J Telomeric trinucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain S 1–136（136 aa）
Chain W 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
7V9K Telomeric tetranucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain S 1–136（136 aa）
Chain W 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.10 Å
7V9S Telomeric trinucleosome in open state Deposited 2021-08-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain S 1–136（136 aa）
Chain W 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7VA4 Telomeric tetranucleosome in open state Deposited 2021-08-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain S 1–136（136 aa）
Chain W 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 14.00 Å
7VZ4 Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA sequence Deposited 2021-11-15 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 1.89 Å
7W9V Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) Deposited 2021-12-10 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
7X57 Cryo-EM structure of human subnucleosome (closed form) Deposited 2022-03-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain C 2–136（135 aa）
Chain E 2–136（135 aa）
Chain G 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.63 Å
7X58 Cryo-EM structure of human subnucleosome (open form) Deposited 2022-03-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain C 2–136（135 aa）
Chain E 2–136（135 aa）
Chain G 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain U 1–136（136 aa）
Chain Y 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.51 Å R-free 0.280
7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Chain e 1–136（136 aa）
Chain i 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.51 Å R-free 0.280
7XVM Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded CA CALCIUM ION × 18 CL CHLORIDE ION × 3 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 2.84 Å R-free 0.259
7XX5 Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded CA CALCIUM ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.19 Å R-free 0.259
7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded CA CALCIUM ION × 21 K POTASSIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.39 Å R-free 0.296
7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain U 1–136（136 aa）
Chain Y 1–136（136 aa）
Chain e 1–136（136 aa）
Chain i 1–136（136 aa）
Not recorded CA CALCIUM ION × 26 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.39 Å R-free 0.296
7XZX Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain Deposited 2022-06-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.53 Å
7XZY Cryo-EM structure of the nucleosome containing 193 base-pair DNA with a p53 target sequence Deposited 2022-06-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
7XZZ Cryo-EM structure of the nucleosome in complex with p53 Deposited 2022-06-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7Y00 Cryo-EM structure of the nucleosome containing 169 base-pair DNA with a p53 target sequence Deposited 2022-06-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
7Y5U Cryo-EM structure of the monomeric human CAF1LC-H3-H4 complex Deposited 2022-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7Y5V Cryo-EM structure of the dimeric human CAF1LC-H3-H4 complex Deposited 2022-06-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain D 1–136（136 aa）
Chain I 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.10 Å
7Y5W Cryo-EM structure of the left-handed Di-tetrasome Deposited 2022-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain C 1–136（136 aa）
Chain E 1–136（136 aa）
Chain G 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7Y60 Cryo-EM structure of human CAF1LC bound right-handed Di-tetrasome Deposited 2022-06-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain C 1–136（136 aa）
Chain E 1–136（136 aa）
Chain G 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7Y61 Cryo-EM structure of the two CAF1LCs bound right-handed Di-tetrasome Deposited 2022-06-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 1–136（136 aa）
Chain C 1–136（136 aa）
Chain E 1–136（136 aa）
Chain G 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
7Y7I chicken KNL2 in complex with the CENP-A nucleosome Deposited 2022-06-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–64（64 aa）
Chain E 1–64（64 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
7YOZ Cryo-EM structure of human subnucleosome (intermediate form) Deposited 2022-08-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain C 2–136（135 aa）
Chain E 2–136（135 aa）
Chain G 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7YQK cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1 Deposited 2022-08-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 37–136（100 aa）
Chain E 37–136（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
7ZI4 Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Deposited 2022-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain I 1–136（136 aa）
Chain M 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；4uL of sample applied to Quantifoil R2/2 Cu 300 mesh grids. blot parameters were wait time 30 sec, blot time 0.5 sec, blot force -8
Resolution 3.20 Å
8DK5 Structure of 187bp LIN28b nucleosome with site 0 mutation Deposited 2022-07-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8EVG 162bp CX3CR1 nucleosome (further classified with better nucleosome end) Deposited 2022-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
8EVH CX3CR1 nucleosome and wild type PU.1 complex Deposited 2022-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
8EVI CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations Deposited 2022-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8EVJ CX3CR1 nucleosome bound PU.1 and C/EBPa Deposited 2022-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8GE0 Crystal structure of JADE1 PZP domain in complex with Histone H3 Deposited 2023-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–14（13 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000
Resolution 2.40 Å R-free 0.241
8GE0 Crystal structure of JADE1 PZP domain in complex with Histone H3 Deposited 2023-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–14（13 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000
Resolution 2.40 Å R-free 0.241
8GE0 Crystal structure of JADE1 PZP domain in complex with Histone H3 Deposited 2023-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 2–14（13 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000
Resolution 2.40 Å R-free 0.241
8GUI Bre1-nucleosome complex (Model I) Deposited 2022-09-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
8GUJ Bre1-nucleosome complex (Model II) Deposited 2022-09-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8GUK Human nucleosome core particle (free form) Deposited 2022-09-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.51 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain a 2–136（135 aa）
Chain e 2–136（135 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain a 2–136（135 aa）
Chain e 2–136（135 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8H1T Cryo-EM structure of BAP1-ASXL1 bound to chromatosome Deposited 2022-10-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8HAG Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (3.2 angstrom resolution) Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8HAH Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (3.9 angstrom resolution) Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8HAI Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (4.7 angstrom resolution) Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
8HAJ Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (4.8 angstrom resolution) Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
8HAK Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (4.5 angstrom resolution) Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
8HAL Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 1 Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8HAM Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 2 Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
8HAN Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 3 Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8IEG Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deposited 2023-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain E 38–135（98 aa）
Chain K 38–135（98 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8IEJ RNF20-RNF40/hRad6A-Ub/nucleosome complex Deposited 2023-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain E 38–135（98 aa）
Chain K 38–135（98 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
8IHL Overlapping tri-nucleosome Deposited 2023-02-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain K 2–136（135 aa）
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Chain U 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.64 Å
8IIY Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K14ac peptide Deposited 2023-02-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–20（19 aa）
Chain C 2–20（19 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris buffer (pH 8.5) containing 20% (w/v) PEG monomethyl ether 2000, 200 mM trimethylamine N-oxide
Resolution 2.15 Å R-free 0.247
8IIZ Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K27ac peptide Deposited 2023-02-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–33（32 aa）
Chain C 2–33（32 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris buffer (pH 8.5) containing 20% (w/v) PEG monomethyl ether 2000, 200 mM trimethylamine N-oxide
Resolution 2.10 Å R-free 0.301
8IJ0 Crystal structure of GAS41 YEATS domain in complex with H3K9ac peptide Deposited 2023-02-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–12（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 3 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Na-HEPES buffer (pH 7.5) containing 5% (w/v) PEG 400 and 2 M ammonium sulfate
Resolution 1.52 Å R-free 0.189
8IJ0 Crystal structure of GAS41 YEATS domain in complex with H3K9ac peptide Deposited 2023-02-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–12（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 3 SO4 SULFATE ION × 4 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Na-HEPES buffer (pH 7.5) containing 5% (w/v) PEG 400 and 2 M ammonium sulfate
Resolution 1.52 Å R-free 0.189
8IQF Cryo-EM structure of the dimeric human CAF1-H3-H4 complex Deposited 2023-03-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain D 1–136（136 aa）
Chain I 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8IQG Cryo-EM structure of the monomeric human CAF1-H3-H4 complex Deposited 2023-03-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8J6S Cryo-EM structure of the single CAF-1 bound right-handed Di-tetrasome Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain C 1–136（136 aa）
Chain E 1–136（136 aa）
Chain G 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8J6T Cryo-EM structure of the double CAF-1 bound right-handed Di-tetrasome Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 1–136（136 aa）
Chain C 1–136（136 aa）
Chain E 1–136（136 aa）
Chain G 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
8JBX Human canonical 601 DNA nucleosome Deposited 2023-05-09 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
8JCC Human histone H2B variant H2BFWT Cryo-EM structure with 601 DNA sequence Deposited 2023-05-10 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
8JCD Human H2BFWTH100R nucleosome with 601 DNA Deposited 2023-05-11 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
8JHF Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.68 Å
8JHG Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.58 Å
8JL9 Cryo-EM structure of the human nucleosome with scFv Deposited 2023-06-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
8JLA Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 Deposited 2023-06-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 29–136（108 aa）
Chain E 29–136（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8JND The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-06-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 19-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
8JNE The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding Deposited 2023-06-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.68 Å
8JNF The cryo-EM structure of the RAD51 filament bound to the nucleosome Deposited 2023-06-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.91 Å
8KCY Structure of nucleosome complexed with two DEK molecules Deposited 2023-08-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8KD1 Structure of nucleosome complexed with one DEK molecule Deposited 2023-08-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8KE0 Structure of H1.2 bound to the nucleosome Deposited 2023-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8OFF Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes (Map1) Deposited 2023-03-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain Ca 1–135（135 aa）
Chain Cb 1–135（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；blot force = 0 N blot time = 8 s
Resolution 3.40 Å
8OO7 CryoEM Structure INO80core Hexasome complex composite model state1 Deposited 2023-04-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
Resolution 2.80 Å
8OOA CryoEM Structure INO80core Hexasome complex Hexasome refinement state1 Deposited 2023-04-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
Resolution 3.18 Å
8OOP CryoEM Structure INO80core Hexasome complex composite model state2 Deposited 2023-04-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 2 ALF TETRAFLUOROALUMINATE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
Resolution 2.70 Å
8OOS CryoEM Structure INO80core Hexasome complex ATPase-hexasome refinement state 2 Deposited 2023-04-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
Resolution 3.29 Å
8OSJ Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Deposited 2023-04-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
8OSK Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) Deposited 2023-04-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8OSL Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement) Deposited 2023-04-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
8OTS OCT4 and MYC-MAX co-bound to a nucleosome Deposited 2023-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8OTT MYC-MAX bound to a nucleosome at SHL+5.8 Deposited 2023-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 40–134（95 aa）
Chain E 40–134（95 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8OX0 Structure of apo telomeric nucleosome Deposited 2023-04-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25 mM HEPES-KOH pH 8.0, 150 mM KCl, 1 mM MgCl2, 1% glycerol, 0.01% Igepal CA-630,1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Blot Force: -15 Blot Time: 2.5 s
Resolution 2.52 Å
8OX1 Structure of TRF1core in complex with telomeric nucleosome Deposited 2023-04-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25 mM HEPES-KOH pH 8.0, 150 mM KCl, 1 mM MgCl2, 1% glycerol, 0.01% Igepal CA-630, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Blot Force: -15 Blot Time: 2.5 s
Resolution 2.70 Å
8Q36 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound) Deposited 2023-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain AAA 39–136（98 aa）
Chain EEE 39–136（98 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0].
Resolution 2.60 Å R-free 0.262
8Q3E High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain AAA 39–136（98 aa）
Chain EEE 39–136（98 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.17 Å R-free 0.270
8Q3M Structure of Nucleosome Core with a Bound Kaposi Sarcoma Associated Herpesvirus LANA Peptide Having a Methionine to Ornithine Substitution Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain AAA 39–136（98 aa）
Chain EEE 39–136（98 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.50 Å R-free 0.268
8Q3X Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound) Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain AAA 39–136（98 aa）
Chain EEE 39–136（98 aa）
Not recorded AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.30 Å R-free 0.262
8QKT Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment Deposited 2023-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain AAA 39–136（98 aa）
Chain EEE 39–136（98 aa）
Not recorded MN MANGANESE (II) ION × 19 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；MnCl2-containing buffers
Resolution 3.26 Å R-free 0.321
8QKT Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment Deposited 2023-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain KKK 39–136（98 aa）
Chain OOO 39–136（98 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；MnCl2-containing buffers
Resolution 3.26 Å R-free 0.321
8RGM Cryo-EM structure of nucleosome containing Widom603 DNA Deposited 2023-12-14 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8SMW Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SMX Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMY Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMZ Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN0 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN1 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SN2 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8SPS High resolution structure of ESRRB nucleosome bound OCT4 at site a and site b Deposited 2023-05-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8SPU Structure of ESRRB nucleosome bound OCT4 at site c Deposited 2023-05-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8SWI Crystal structure of legAS4 from Legionella pneumophila subsp. pneumophila with histone H3 (1-12)peptide Deposited 2023-05-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–13（12 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M Bis-Tris 6.5 and 38% PPG P400
Resolution 3.00 Å R-free 0.310
8SYP Genomic CX3CR1 nucleosome Deposited 2023-05-25 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8TXV Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Deposited 2023-08-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TXW Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Deposited 2023-08-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TXX Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Deposited 2023-08-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8U13 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) Deposited 2023-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8U14 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Deposited 2023-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8U9S Cryo-EM structure of NRCAM nucleosome aided by scFv Deposited 2023-09-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8UBJ Cryo-EM structure of NRCAM nucleosome aided by scFv (3D Flex map) Deposited 2023-09-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8UBK Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome Deposited 2023-09-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8UBL Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome (3D Flex map) Deposited 2023-09-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8UPF Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Deposited 2023-10-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8VFX Cryo-EM structure of 186bp ALBN1 nucleosome aided by scFv Deposited 2023-12-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
8VFY Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1) Deposited 2023-12-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
8VFZ Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2) Deposited 2023-12-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8VG0 Cryo-EM structure of GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8VG1 Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
8VG2 Cryo-EM structure of FoxA1 and GATA4 in complex with H14 chromatosome Deposited 2023-12-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8VLR Cryo-EM structure of native H2AK119bu nucleosome at 2.6 Deposited 2024-01-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 39–136（98 aa）
Chain E 39–136（98 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Tris-HCl, pH 7.5, 50 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8VMI PRC2_AJ119-450 bound to H3K4me3 Deposited 2024-01-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 2–7（6 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VML PRC2_AJ1-450 bound to H3K4me3 Deposited 2024-01-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain I 20–41（22 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8VNV PRC2_AJ1-450 bound to H3K36me3 with histone H3 tail engaged Deposited 2024-01-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain I 20–41（22 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8W9D Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8W9E Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8W9F Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 38–135（98 aa）
Chain E 38–135（98 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8X15 Structure of nucleosome-bound SRCAP-C in the apo state Deposited 2023-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain C 1–136（136 aa）
Chain G 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8X19 Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state Deposited 2023-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain C 1–136（136 aa）
Chain G 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8X1C Structure of nucleosome-bound SRCAP-C in the ADP-bound state Deposited 2023-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain C 1–136（136 aa）
Chain G 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8XBT The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.12 Å
8XBU The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.24 Å
8XBW The cryo-EM structure of the RAD51 N-terminal lobe domain bound to the histone H4 tail of the nucleosome Deposited 2023-12-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain a 2–136（135 aa）
Chain e 2–136（135 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain a 2–136（135 aa）
Chain e 2–136（135 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8Y3C Cryo-EM structure of the overlapping di-nucleosome (closed form) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.21 Å
8Y3D Cryo-EM structure of the overlapping di-nucleosome (intermediate form2) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
8Y3E Cryo-EM structure of the overlapping di-nucleosome (open form) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.32 Å
8Y3F Cryo-EM structure of the overlapping di-nucleosome (intermediate form1) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.54 Å
8YBJ Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence Deposited 2024-02-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.38 Å
8YBK Cryo-EM structure of the human nucleosome containing the H3.1 E97K mutant Deposited 2024-02-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：E97K Mutation：E97K No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.69 Å
8YJF Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and an H2A-H2B dimer Deposited 2024-03-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 57–136（80 aa）
Chain E 57–136（80 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M calcium acetate, 0.1 M Sodium cacodylate pH 5.5, 12% (w/v) PEG 8000
Resolution 4.40 Å R-free 0.312
8YJM Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and a single chain H2B-H2A chimera Deposited 2024-03-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 57–136（80 aa）
Chain E 57–136（80 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.2 M sodium acetate, 0.1 M sodium citrate pH 5.5, 5%(w/v) PEG 4000
Resolution 4.15 Å R-free 0.286
8YNY Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome Deposited 2024-03-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: 13-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.52 Å
8YTI Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2024-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded CL CHLORIDE ION × 8 CA CALCIUM ION × 52 K POTASSIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45 mM CaCl2, 25 mM KCl, 10 mM Na-acetate (pH 4.5)
Resolution 2.70 Å R-free 0.267
8YV8 Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence. Deposited 2024-03-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9ECP Structure of the native human NCP purified from HEK293 cells Deposited 2024-11-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 39–134（96 aa）
Chain E 39–134（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.91 Å
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Q 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Z 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain a 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain b 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 13 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain c 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 14 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain d 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 15 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain e 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 16 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain f 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain S 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain T 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain U 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain V 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain W 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Y 16–22（7 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
Resolution 2.60 Å R-free 0.267
9FGQ Structure of human APC3loop 375-381 bound to the NCP Deposited 2024-05-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPEs pH8.0, 50 mM NaCl, 0.5 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9FH9 Structure of CyclinB1 N-terminus bound to the NCP Deposited 2024-05-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9GCG CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Deposited 2024-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain M 1–136（136 aa）
Chain Q 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å
9GE4 CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Deposited 2024-08-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 1–136（136 aa）
Chain Q 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
9GE5 CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain M 43–136（94 aa）
Chain Q 43–136（94 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
9GEL CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain M 1–136（136 aa）
Chain Q 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.86 Å
9GEV CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain M 1–136（136 aa）
Chain Q 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9GF6 CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain M 1–136（136 aa）
Chain Q 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9GFB CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain M 1–136（136 aa）
Chain Q 1–136（136 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
9GFM CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain M 44–136（93 aa）
Chain Q 37–136（100 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9IGW Ku70/80 bound to 147 bp nucleosome Deposited 2025-02-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
9IGX Ku70/80 bound to 153 bp nucleosome Deposited 2025-02-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 39–135（97 aa）
Chain E 39–135（97 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å
9J8M Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (High mobility complex) Deposited 2024-08-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.82 Å
9J8N Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (Low mobility complex) Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 32-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.14 Å
9J8O Cryo-EM structure of BAF-Lamin A/C IgF-H1-nucleosome complex Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 28-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
9J8W Cryo-EM structure of NCP-UV-DDB complex containing CPD Deposited 2024-08-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
9JC6 Human H2BW2 nucleosome Deposited 2024-08-28 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
9MLL GammaH2AX containing nucleosomes, Parallel stack Deposited 2024-12-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain L 1–136（136 aa）
Chain P 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9MLN GammaH2AX containing nucleosome, Canonical (Class 1) Deposited 2024-12-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9MLR GammaH2AX containing nucleosome, Half-wrapped (Class 2) Deposited 2024-12-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9MLS GammaH2AX containing nucleosome, Extended (Class 3) Deposited 2024-12-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9MMK H2AX containing nucleosome, Canonical (Class 1) Deposited 2024-12-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9MMM H2AX containing nucleosomes, Parallel stack Deposited 2024-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain L 1–136（136 aa）
Chain P 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9MMN H2AX containing nucleosomes, Left offset stack Deposited 2024-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain L 1–136（136 aa）
Chain P 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9MMO H2AX containing nucleosomes, Right offset stack Deposited 2024-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain L 1–136（136 aa）
Chain P 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9MMT H2AX containing nucleosome, Unwrapped (Class 2) Deposited 2024-12-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9Q80 Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome Deposited 2025-02-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9Q8X Ku70/80 bound to a 153 bp H2AX nucleosome Deposited 2025-02-25 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
9Q9F DNA-PK bound to a 153 bp H2AX nucleosome model 1 Deposited 2025-02-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.54 Å
9QCR DNA-PK bound to 153 bp H2AX nucleosome model 2 Deposited 2025-03-05 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.37 Å
9QCS Ku80 mediated DNA-PK dimer bound to 153 bp H2AX nucleosome Deposited 2025-03-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 26-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
9QLM Solution structure of the TAF3-PHD bound to a H3K4me3Q5ser histone tail peptide with a serotonylated glutamine Deposited 2025-03-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–13（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 SRO SEROTONIN × 1 SOLUTION NMR
NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 44；Pressure 1
NMR sample composition 0.88 mM [U-13C; U-15N] TAF3-PHD, 0.88 mM H3K4me3Q5ser, 20 mM potassium phosphate, 4 mM potassium chloride, 10 uM zinc chloride, 0.01 % w/v sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
9QMS DNA-PK bound to 153 bp H2AX nucleosome with ATPyS Deposited 2025-03-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 30-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
9R04 p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample) Deposited 2025-04-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9R2M p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, composite map) Deposited 2025-04-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9R2P p53 bound to nucleosome at position SHL+5.9 (crosslinked sample) Deposited 2025-04-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
9R2Q p53 bound to nucleosome at position SHL-5.7 (non-crosslinked sample) Deposited 2025-04-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9RL4 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2025-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded PTD PENTANEDIAL × 16 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9RMC Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1 Deposited 2025-06-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9RN1 Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2 Deposited 2025-06-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
9RN2 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 Deposited 2025-06-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain a 1–136（136 aa）
Chain c 1–136（136 aa）
Chain e 1–136（136 aa）
Chain g 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain e 1–136（136 aa）
Chain g 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.54 Å
9UZ7 Cryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking Deposited 2025-05-16 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain B 2–136（135 aa）
Mutation：C96S/C110S/K115C Mutation：C96S/C110S/K115C Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；10 mM HEPES, pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution not provided
9V6Q Cryo-EM structure of two cPRC1 complexes bound to opposite faces of an endogenous 147-bp mono-nucleosome Deposited 2025-05-27 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.60 Å
9V6S Cryo-EM structure of a single cPRC1 complex engaged on one face of an endogenous 147-bp mononucleosome Deposited 2025-05-27 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
9V6X Cryo-EM structure of the cPRC1 complex bound to an endogenous 184-bp mono-nucleosome Deposited 2025-05-27 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.00 Å
9V8L Cryo-EM structure of the cPRC1-di-nucleosome (loose) complex Deposited 2025-05-29 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 6.60 Å
9V9H Cryo-EM structure of the cPRC1-di-nucleosome (tight) complex Deposited 2025-05-30 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain M 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.50 Å
9V9P Cryo-EM structure of the cPRC1-di-nucleosome (CBX7) complex Deposited 2025-06-01 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain M 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.40 Å
9VEM SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 1 Deposited 2025-06-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 17–22（6 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Tris 8.0, 25% PEG 2000MME
Resolution 2.57 Å R-free 0.264
9VEW SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 2 Deposited 2025-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 16–22（7 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Tris 8.0, 25% PEG 2000MME
Resolution 2.68 Å R-free 0.251
9VG0 SIRT2 structure in complex with H3K18myr peptide Deposited 2025-06-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 16–22（7 aa）
Not recorded EDO 1,2-ETHANEDIOL × 5 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；Tris 8.0, 25% PEG 2000MME
Resolution 1.61 Å R-free 0.231
9VG3 SIRT2 structure in complex with H3K18myr peptide: pre NAD binding state Deposited 2025-06-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 17–22（6 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；Tris 8.0, 25% PEG2000MME
Resolution 2.15 Å R-free 0.251
9VGE SIRT2 demyristoylation intermediate I structure Deposited 2025-06-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 16–22（7 aa）
Not recorded NCA NICOTINAMIDE × 1 GOL GLYCEROL × 1 ZN ZINC ION × 1 YDD [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4-bis(oxidanyl)-5-tetradecoxy-oxolan-2-yl]methyl hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；Tris 8.0, 25% PEG 2000MME
Resolution 2.56 Å R-free 0.282
9VGZ SIRT2-F96A structure in complex with H3K18myr peptide and native NAD Deposited 2025-06-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 16–22（7 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；Tris 8.0, 25% PEG 2000MME
Resolution 2.34 Å R-free 0.236
9VH0 SIRT2-H187A structure in complex with H3K18myr peptide and native NAD Deposited 2025-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 16–21（6 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；0.1 M MES 5.5, 9.2% PEG10000
Resolution 2.41 Å R-free 0.273
9VH0 SIRT2-H187A structure in complex with H3K18myr peptide and native NAD Deposited 2025-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 16–21（6 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；0.1 M MES 5.5, 9.2% PEG10000
Resolution 2.41 Å R-free 0.273
9XSF Cryo-EM structure of H4S47GlcNAc nucleosome at 3.39 angstrom Deposited 2025-11-20 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.39 Å
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å
9ZEO Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1 Deposited 2025-11-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 39–136（98 aa）
Chain E 39–136（98 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

402 other PDB entries and 475 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H31_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain A； PDBConstruct 1–135； UniProt 2–136 Author chain E； PDBConstruct 1–135； UniProt 2–136

Histone H4

Homo sapiens

UniProt P62805

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 15 DNA 2 PDB declaration: 17-meric（17） Consistent with all polymer counts Chain B； UniProt 2–103 Chain F； UniProt 2–103 Not recorded Ubiquitin × 1 （P0CG47） [histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D × 1 （A0A6P6IDI8,O14686） Retinoblastoma-binding protein 5 × 1 （Q15291） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H3.1 × 2 （P68431） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 2-E × 2 （Q16778） DNA (145-MER) × 1 WD repeat-containing protein 5 × 1 （P61964） DNA (145-MER) × 1 Protein dpy-30 homolog × 2 （Q9C005） ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.63 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9YLE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10XZ Non-damaged nucleosome Deposited 2026-02-12 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
10YA Nucleosome containing a nick at SHL-4 Deposited 2026-02-12 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
10YB Nucleosome containing a nick at SHL-2 Deposited 2026-02-12 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
10YC Nucleosome containing a nick at SHL-4 Deposited 2026-02-12 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
10YD Nucleosome containing a nick at SHL-6 Deposited 2026-02-12 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
10YE DNA Ligase IIIa bound to nucleosome containing a nick at SHL0 Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 23–102（80 aa）
Chain F 23–102（80 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
10YF DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (composite) Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 23–102（80 aa）
Chain F 23–102（80 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution not provided
10YG DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-4 (composite) Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 23–102（80 aa）
Chain F 23–102（80 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution not provided
10YH DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 (composite) Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 23–102（80 aa）
Chain F 23–102（80 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
10YI XRCC1-DNA Ligase IIIa complex bound to a nucleosome containing a nick at SHL-6 (composite) Deposited 2026-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 23–102（80 aa）
Chain F 23–102（80 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
2BQZ Crystal structure of a ternary complex of the human histone methyltransferase Pr-SET7 (also known as SET8) Deposited 2005-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 17–25（9 aa） Fragment：RESIDUES 17-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.00
Resolution 1.50 Å R-free 0.206
2BQZ Crystal structure of a ternary complex of the human histone methyltransferase Pr-SET7 (also known as SET8) Deposited 2005-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 17–25（9 aa） Fragment：RESIDUES 17-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.00
Resolution 1.50 Å R-free 0.206
2CV5 Crystal structure of human nucleosome core particle Deposited 2005-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 0–102（103 aa）
Chain F 0–102（103 aa）
Not recorded MN MANGANESE (II) ION × 9 CL CHLORIDE ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.277
2LVM Solution structure of human 53BP1 tandem Tudor domains in complex with a histone H4K20me2 peptide Deposited 2012-07-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 15–28（14 aa） Fragment：UNP residues 15-28
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 1.7 mM [U-100% 13C; U-100% 15N] protein_1, 8.5 mM protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.7 mM [U-100% 13C; U-100% 15N] protein_1, 8.5 mM protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 100% D2O | 100% D2O
NMR sample composition 5 mM protein_1, 4 mM [U-100% 13C; U-100% 15N] protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 5 mM protein_1, 4 mM [U-100% 13C; U-100% 15N] protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 100% D2O | 100% D2O
Resolution not provided
2RNY Complex Structures of CBP Bromodomain with H4 ack20 Peptide Deposited 2008-02-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 14–28（15 aa） Fragment：UNP residues 14-28
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition 0.5mM [U-100% 13C; U-100% 15N] sodium phosphate, 100% D2O | 100% D2O
Resolution not provided
2RS9 Solution structure of the bromodomain of human BRPF1 in complex with histone H4K5ac peptide Deposited 2011-12-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–11（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；288 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition 1.5 mM H4K5ac-1, 0.54 mM [U-99% 13C; U-99% 15N] Bromodomain-2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3A6N The nucleosome containing a testis-specific histone variant, human H3T Deposited 2009-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.264
3AFA The human nucleosome structure Deposited 2010-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.270
3AV1 The human nucleosome structure containing the histone variant H3.2 Deposited 2011-02-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.290
3AV2 The human nucleosome structure containing the histone variant H3.3 Deposited 2011-02-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.272
3AYW Crystal Structure of Human Nucleosome Core Particle Containing H3K56Q mutation Deposited 2011-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.90 Å R-free 0.273
3AZE Crystal Structure of Human Nucleosome Core Particle Containing H3K64Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.302
3AZF Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.263
3AZG Crystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.40 Å R-free 0.269
3AZH Crystal Structure of Human Nucleosome Core Particle Containing H3K122Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.49 Å R-free 0.266
3AZI Crystal Structure of Human Nucleosome Core Particle Containing H4K31Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：K31Q Mutation：K31Q CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.289
3AZJ Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：K44Q Mutation：K44Q CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.89 Å R-free 0.268
3AZK Crystal Structure of Human Nucleosome Core Particle Containing H4K59Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：K59Q Mutation：K59Q CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.20 Å R-free 0.258
3AZL Crystal Structure of Human Nucleosome Core Particle Containing H4K77Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：K77Q Mutation：K77Q CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.259
3AZM Crystal Structure of Human Nucleosome Core Particle Containing H4K79Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：K79Q Mutation：K79Q CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.89 Å R-free 0.296
3AZN Crystal Structure of Human Nucleosome Core Particle Containing H4K91Q mutation Deposited 2011-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：K91Q Mutation：K91Q CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.254
3CFS Structural basis of the interaction of RbAp46/RbAp48 with histone H4 Deposited 2008-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 28–42（15 aa） Fragment：UNP residues 28 to 42
Not recorded ARS ARSENIC × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；277 K；18% PEG8000, 0.2M Ca acetate, 0.1M Na Cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.40 Å R-free 0.249
3CFV Structural basis of the interaction of RbAp46/RbAp48 with histone H4 Deposited 2008-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 25–42（18 aa） Fragment：UNP residues 25 to 42
Not recorded ARS ARSENIC × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；13% PEG 2000, 0.2M Ca acetate, 0.1M Na Cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.60 Å R-free 0.257
3CFV Structural basis of the interaction of RbAp46/RbAp48 with histone H4 Deposited 2008-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 25–42（18 aa） Fragment：UNP residues 25 to 42
Not recorded ARS ARSENIC × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；13% PEG 2000, 0.2M Ca acetate, 0.1M Na Cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.60 Å R-free 0.257
3F9W Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.206
3F9W Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.206
3F9W Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.206
3F9W Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.206
3F9X Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me2 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 16–25（10 aa） Fragment：UNP residues 16-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.25 Å R-free 0.207
3F9X Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me2 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 16–25（10 aa） Fragment：UNP residues 16-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.25 Å R-free 0.207
3F9X Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me2 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 16–25（10 aa） Fragment：UNP residues 16-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.25 Å R-free 0.207
3F9X Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me2 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 16–25（10 aa） Fragment：UNP residues 16-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.25 Å R-free 0.207
3F9Y Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me1 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 16–25（10 aa） Fragment：UNP residues 16-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.220
3F9Y Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me1 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 16–25（10 aa） Fragment：UNP residues 16-25
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.220
3F9Z Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.257
3F9Z Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.257
3F9Z Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.257
3F9Z Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy Deposited 2008-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 16–25（10 aa） Fragment：UNP residues 16-25
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.257
3NQJ Crystal structure of (CENP-A/H4)2 heterotetramer Deposited 2010-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 21–103（83 aa） Fragment：UNP residues 21-103
Not recorded PO4 PHOSPHATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.17 M ammonium sulfate, 0.085 M sodium cacodylate (pH 6.5), 25.5% PEG-8000, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.10 Å R-free 0.241
3NQU Crystal structure of partially trypsinized (CENP-A/H4)2 heterotetramer Deposited 2010-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–103（103 aa）
Not recorded SO4 SULFATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；295 K；2 M ammonium sulfate, 0.1 M HEPES (pH 7.9), VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.50 Å R-free 0.302
3O36 Crystal structure of TRIM24 PHD-Bromo complexed with H4(14-19)K16ac peptide Deposited 2010-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 15–20（6 aa） Fragment：UNP residues 15-20
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50 mM Bis-Tris (pH 6.5), 30% Polyethylene glycol 3350, 100 mM ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.216
3O36 Crystal structure of TRIM24 PHD-Bromo complexed with H4(14-19)K16ac peptide Deposited 2010-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 15–20（6 aa） Fragment：UNP residues 15-20
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50 mM Bis-Tris (pH 6.5), 30% Polyethylene glycol 3350, 100 mM ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.216
3QZS Crystal Structure of BPTF bromo in complex with histone H4K16ac - Form I Deposited 2011-03-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 13–22（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；100 mM Tris-HCl pH 8.0, 20% Glycerol, vapor diffusion, hanging drop
Resolution 1.80 Å R-free 0.230
3QZS Crystal Structure of BPTF bromo in complex with histone H4K16ac - Form I Deposited 2011-03-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 13–22（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；100 mM Tris-HCl pH 8.0, 20% Glycerol, vapor diffusion, hanging drop
Resolution 1.80 Å R-free 0.230
3QZT Crystal Structure of BPTF bromo in complex with histone H4K16ac - Form II Deposited 2011-03-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 13–22（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；20% (W/V) PEGMME 2K, 20% Glycerol and 0.2 M KCl, 0.1 M Tris-HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.50 Å R-free 0.198
3QZV Crystal Structure of BPTF PHD-linker-bromo in complex with histone H4K12ac peptide Deposited 2011-03-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 8–18（11 aa） Fragment：Histone H4 7-17
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% (W/V) PEG3000, 0.3 M NaAcetate, 0.1 M Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.234
3R45 Structure of a CENP-A-Histone H4 Heterodimer in complex with chaperone HJURP Deposited 2011-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–103（103 aa）
Not recorded SO4 SULFATE ION × 13 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；2M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.60 Å R-free 0.245
3UVW Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K5acK8ac) Deposited 2011-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–12（11 aa） Fragment：unp residues 2-12
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；278 K；0.1M Tris, 20% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 278K, pH 8.0
Resolution 1.37 Å R-free 0.171
3UVY Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K16acK20ac) Deposited 2011-11-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 16–26（11 aa） Fragment：UNP RESIDUES 16-26
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；278 K；0.2M NaI, 0.1M BTProp, 20% PEG 3350, 10% EtGly, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Resolution 2.02 Å R-free 0.258
3UW9 Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K8acK12ac) Deposited 2011-12-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 8–18（11 aa） Fragment：unp residues 8-18
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1M Tris, 0.3M LiCl 15% PEG6000, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 8.0
Resolution 2.30 Å R-free 0.257
3UW9 Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K8acK12ac) Deposited 2011-12-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 8–18（11 aa） Fragment：unp residues 8-18
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1M Tris, 0.3M LiCl 15% PEG6000, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 8.0
Resolution 2.30 Å R-free 0.257
3W96 Crystal Structure of Human Nucleosome Core Particle lacking H2A N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.296
3W97 Crystal Structure of Human Nucleosome Core Particle lacking H2B N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.20 Å R-free 0.321
3W98 Crystal Structure of Human Nucleosome Core Particle lacking H3.1 N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.42 Å R-free 0.303
3W99 Crystal Structure of Human Nucleosome Core Particle lacking H4 N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 17–103（87 aa） Fragment：UNP residues 17-103
Chain F 17–103（87 aa） Fragment：UNP residues 17-103
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.312
3WA9 The nucleosome containing human H2A.Z.1 Deposited 2013-04-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.07 Å R-free 0.271
3WAA The nucleosome containing human H2A.Z.2 Deposited 2013-04-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.271
3WKJ The nucleosome containing human TSH2B Deposited 2013-10-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.291
3WTP Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3 Deposited 2014-04-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, vapor diffusion, hanging drop, temperature 293K
Resolution 2.67 Å R-free 0.270
3X1S Crystal structure of the nucleosome core particle Deposited 2014-11-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70mM KCL, 70-90mM MnCl2, 24% MPD, 20mM Na-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.81 Å R-free 0.270
3X1T Crystal structure of nucleosome core particle consisting of mouse testis specific histone variants H2aa and H2ba Deposited 2014-11-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 22 CL CHLORIDE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70mM Kcl, 70-90mM MnCl2, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.81 Å R-free 0.266
3X1U Crystal structure of nucleosome core particle in the presence of histone variants involved in reprogramming Deposited 2014-11-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 4 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70 mM KCl, 70-90 mM MnCl2, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.25 Å R-free 0.270
3X1V Crystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming Deposited 2014-11-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 19 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70 mM KCl, 70-90 mM MnCl2, Na-cocodylate, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.92 Å R-free 0.259
4GQB Crystal Structure of the human PRMT5:MEP50 Complex Deposited 2012-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 2–22（21 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 0XU (2S,5S,6E)-2,5-diamino-6-[(3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxydihydrofuran-2(3H)-ylidene]hexanoic acid × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20-30% PEG3350, 100-250 mM ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.06 Å R-free 0.222
4H9N Complex structure 1 of DAXX/H3.3(sub5)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.209
4H9O Complex structure 2 of DAXX/H3.3(sub5,G90M)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.05 Å R-free 0.225
4H9P Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.8 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.242
4H9P Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.8 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.242
4H9Q Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.221
4H9Q Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 18 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.221
4H9R Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.6 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.230
4H9R Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.6 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.230
4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 21–103（83 aa）
Not recorded PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.250
4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 21–103（83 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.250
4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 21–103（83 aa）
Chain D 21–103（83 aa）
Not recorded PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.250
4HGA Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX Deposited 2012-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–103（103 aa）
Not recorded PC4 TETRACHLOROPLATINATE(II) × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；298 K；0.1M HEPES-Na, pH 7.6, 23% (v/v) PEG 3350, 0.25M Ammonium acetate, 1% Tacsimate pH 7.0, 6% ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.80 Å R-free 0.271
4M38 Crystal structure of Trypanosoma brucei protein arginine methyltransferase 7 complex with AdoHcy and histone H4 peptide Deposited 2013-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 2–22（21 aa） Fragment：UNP residues 2-22
Chain F 2–22（21 aa） Fragment：UNP residues 2-22
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；100mM MES, 20% PEG 1000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.230
4QUT Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) complexed with Histone H4-K(ac)12 Deposited 2014-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 7–13（7 aa） Fragment：histone H4 tail
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277.15 K；apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 28-32% PEG 3350, 50 mM bis-tris pH 5.5, 50 mM ammonium phosphate and 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Resolution 1.70 Å R-free 0.180
4QUU Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) complexed with Histone H4-K(ac)5 Deposited 2014-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–13（13 aa） Fragment：histone H4 tail
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277.15 K；apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 28-32% PEG 3350, 50 mM bis-tris pH 5.5, 50 mM ammonium phosphate and 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Resolution 1.80 Å R-free 0.200
4QYD Crystal Structure of the human BRPF1 bromodomain in complex with a histone H4K12ac peptide Deposited 2014-07-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 5–18（14 aa） Fragment：histone H4K12ac peptide (UNP residues 5-18)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；277 K；0.1 M HEPES, pH 7.5, 10% w/v polyethylene glycol (PEG) 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.94 Å R-free 0.213
4YM5 Crystal structure of the human nucleosome containing 6-4PP (inside) Deposited 2015-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 4.00 Å R-free 0.289
4YM6 Crystal structure of the human nucleosome containing 6-4PP (outside) Deposited 2015-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.51 Å R-free 0.287
4YY6 Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Z 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；277 K；0.2 M sodium malonate, pH 4.0, 20% w/v PEG3350
Resolution 1.45 Å R-free 0.208
4YYD Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Z 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M sodium malonate, pH 7.0, 20% w/v PEG3350
Resolution 1.52 Å R-free 0.226
4YYG Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.05 M calcium chloride dihydrate, 0.1 M Bis-Tris, pH 6.5, 30% v/v PEG550 MME
Resolution 2.10 Å R-free 0.311
4YYH Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Z 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M sodium citrate, pH 5.5, 0.2 M sodium chloride, 20% w/v PEG3350
Resolution 1.74 Å R-free 0.260
4YYH Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Y 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M sodium citrate, pH 5.5, 0.2 M sodium chloride, 20% w/v PEG3350
Resolution 1.74 Å R-free 0.260
4YYI Crystal structure of BRD9 Bromodomain bound to an acetylated peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M Bis-Tris, pH 6.5, 25% w/v PEG3350
Resolution 1.50 Å R-free 0.242
4YYI Crystal structure of BRD9 Bromodomain bound to an acetylated peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M Bis-Tris, pH 6.5, 25% w/v PEG3350
Resolution 1.50 Å R-free 0.242
4YYJ Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M ammonium chloride, 20% w/v PEG3350
Resolution 1.85 Å R-free 0.244
4YYJ Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M ammonium chloride, 20% w/v PEG3350
Resolution 1.85 Å R-free 0.244
4YYK Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M MES, pH 6.5, 15% w/v PEG550 MME
Resolution 1.79 Å R-free 0.261
4YYK Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M MES, pH 6.5, 15% w/v PEG550 MME
Resolution 1.79 Å R-free 0.261
4YYM Crystal structure of TAF1 BD2 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Z 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M calcium chloride, 20 w/v PEG3350
Resolution 1.50 Å R-free 0.261
4YYN Crystal structure of TAF1 BD2 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Z 2–12（11 aa） Fragment：N-terminal tail (UNP residues 2-12)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M calcium acetate, 20% w/v PEG3350
Resolution 1.85 Å R-free 0.243
4Z2M Crystal structure of human SPT16 Mid-AID/H3-H4 tetramer FACT Histone complex Deposited 2015-03-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 1–103（103 aa）
Chain J 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；10% PEG400, 0.9-1.1 M Imidazole, 100-150 mM L-histidine
Resolution 2.98 Å R-free 0.246
4Z5T The nucleosome containing human H3.5 Deposited 2015-04-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.80 Å R-free 0.269
5AV5 human nucleosome core particle Deposited 2015-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions LIQUID DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.233
5AV6 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.229
5AV8 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.233
5AV9 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.239
5AVB human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.236
5AVC human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.238
5AY8 Crystal structure of human nucleosome containing H3.Y Deposited 2015-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；sodium acetate, manganese chloride, 2-propanol, trimethylamine N-oxide
Resolution 2.80 Å R-free 0.249
5B0Y Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122 Deposited 2015-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.56 Å R-free 0.249
5B0Z The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution Deposited 2015-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 1.99 Å R-free 0.254
5B24 The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer Deposited 2015-12-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.60 Å R-free 0.249
5B2I Human nucleosome containing CpG unmethylated DNA Deposited 2016-01-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 3.00 Å R-free 0.257
5B2J Human nucleosome containing CpG methylated DNA Deposited 2016-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.60 Å R-free 0.252
5B31 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1. Deposited 2016-02-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.20 Å R-free 0.271
5B32 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3. Deposited 2016-02-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.35 Å R-free 0.259
5B33 The crystal structure of the H2AZ nucleosome with H3.3. Deposited 2016-02-08 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.92 Å R-free 0.252
5B40 The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations Deposited 2016-03-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：K31C Mutation：K31C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；90mM Tris-HCl (pH 7.8), 3.6% PGA-LM, 25.2% PEG 400, 2-6% Pentaerythritol ethoxylate (3/4 EO/OH)
Resolution 3.33 Å R-free 0.263
5BNV Crystal structure of Human MCM2 HBD chaperoning a histone H3-H4 tetramer Deposited 2015-05-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 2–103（102 aa）
Chain E 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5 M sodium/potassium phosphate, pH 8.0
Resolution 2.79 Å R-free 0.220
5BNX Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.3-H4 dimer Deposited 2015-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–103（102 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；3.2 M sodium formate, 0.1 M Tris, pH 8.5
Resolution 2.31 Å R-free 0.213
5BO0 Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.2-H4 dimer Deposited 2015-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–103（102 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；3.2 M sodium formate, 0.1 M Tris, pH 8.5
Resolution 2.91 Å R-free 0.238
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain K 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain O 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain S 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain W 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
Resolution 3.50 Å R-free 0.253
5CPI Nucleosome containing unmethylated Sat2R DNA Deposited 2015-07-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.90 Å R-free 0.295
5CPJ Nucleosome containing methylated Sat2R DNA Deposited 2015-07-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.15 Å R-free 0.295
5CPK Nucleosome containing methylated Sat2L DNA Deposited 2015-07-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.63 Å R-free 0.284
5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 2–21（20 aa） Fragment：DNA binding residues 2-21
Not recorded MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
Resolution 2.34 Å R-free 0.221
5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 2–21（20 aa） Fragment：DNA binding residues 2-21
Not recorded MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
Resolution 2.34 Å R-free 0.221
5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 2–21（20 aa） Fragment：DNA binding residues 2-21
Not recorded MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
Resolution 2.34 Å R-free 0.221
5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–21（20 aa） Fragment：DNA binding residues 2-21
Not recorded MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
Resolution 2.34 Å R-free 0.221
5FWE JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15)R3me2s PEPTIDE Deposited 2016-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–16（15 aa） Fragment：HISTONE H4(1-15)R3ME2S PEPTIDE, UNP RESIDUES 2-16
Non-standard monomer：Yes (specific site not provided by mmCIF) NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；SITTING DROPS, 277 K, 0.15 M POTASSIUM BROMIDE, 30 % W/V PEG 2000 MME, pH 7.5
Resolution 2.05 Å R-free 0.255
5FWE JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15)R3me2s PEPTIDE Deposited 2016-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–16（15 aa） Fragment：HISTONE H4(1-15)R3ME2S PEPTIDE, UNP RESIDUES 2-16
Non-standard monomer：Yes (specific site not provided by mmCIF) NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；SITTING DROPS, 277 K, 0.15 M POTASSIUM BROMIDE, 30 % W/V PEG 2000 MME, pH 7.5
Resolution 2.05 Å R-free 0.255
5GSE Crystal structure of unusual nucleosome Deposited 2016-08-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；potassium bromide, potassium thiocyanate, Tris-HCl, PGA-LM, PEG 400
Resolution 3.14 Å R-free 0.255
5GSU Crystal structure of nucleosome core particle consisting of human testis-specific histone variants, Th2A and Th2B Deposited 2016-08-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20mM Pottasium Cacodylate pH 6.0, 60-70mM KCl, 70-90mM MnCl2
Resolution 3.10 Å R-free 0.257
5GT0 Crystal structure of nucleosome complex with human testis-specific histone variants, Th2a Deposited 2016-08-18 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 14 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；60-70mM KCl, 70-90mM MnCl2, 24% MPD
Resolution 2.82 Å R-free 0.280
5GT3 Crystal structure of nucleosome particle in the presence of human testis-specific histone variant, hTh2b Deposited 2016-08-18 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 12 CL CHLORIDE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；60-70mM KCl, 70-90mM MnCl2, 24% MPD
Resolution 2.91 Å R-free 0.258
5GTC Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle Deposited 2016-08-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.70 Å R-free 0.267
5GXQ The crystal structure of the nucleosome containing H3.6 Deposited 2016-09-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.85 Å R-free 0.262
5JA4 Crystal structure of human TONSL and MCM2 HBDs binding to a histone H3-H4 tetramer Deposited 2016-04-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 2–103（102 aa）
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；0.1M MES pH 5.6, 7% isopropanol
Resolution 2.42 Å R-free 0.246
5JRG Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF) Deposited 2016-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.50 Å R-free 0.245
5KDM Crystal structure of EBV tegument protein BNRF1 in complex with histone chaperone DAXX and histones H3.3-H4 Deposited 2016-06-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；0.1M MES pH 6.0, 0.8 M ammonium sulfate
Resolution 3.50 Å R-free 0.280
5X7X The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution Deposited 2017-02-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.18 Å R-free 0.256
5XF3 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RRK (1R,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
Resolution 2.60 Å R-free 0.270
5XF4 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (S,S-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 SSK (1S,2S)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
Resolution 2.87 Å R-free 0.266
5XF5 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,S-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RSK (1S,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55mM MnCl2, 25-49mM KCl, 20mM K-Cacodylate pH 6.0
Resolution 2.82 Å R-free 0.264
5Y0C Crystal Structure of the human nucleosome at 2.09 angstrom resolution Deposited 2017-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 10 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.09 Å R-free 0.249
5Y0D Crystal Structure of the human nucleosome containing the H2B E76K mutant Deposited 2017-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 1.99 Å R-free 0.252
5Z23 Crystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD Deposited 2017-12-28 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.73 Å R-free 0.261
5Z30 The crystal structure of the nucleosome containing a cancer-associated histone H2A.Z R80C mutant Deposited 2018-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.45 Å R-free 0.243
5ZBX The crystal structure of the nucleosome containing histone H3.1 CATD(V76Q, K77D) Deposited 2018-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.58 Å R-free 0.249
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6BUZ Cryo-EM structure of CENP-A nucleosome in complex with kinetochore protein CENP-N Deposited 2017-12-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
6C0W Cryo-EM structure of human kinetochore protein CENP-N with the centromeric nucleosome containing CENP-A Deposited 2018-01-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6E0C Cryo-EM structure of the CENP-A nucleosome (W601) in complex with a single chain antibody fragment Deposited 2018-07-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.63 Å
6E0P Cryo-EM structure of the centromeric nucleosome (Native alpha satellite DNA) in complex with a single chain antibody fragment Deposited 2018-07-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；blot for 2.5 sec before plunging
Resolution 2.60 Å
6FML CryoEM Structure INO80core Nucleosome complex Deposited 2018-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8, 60 mM KCl, 0.5% glycerol, 0.25 mM CaCl2, 20 uM ZnCl2, 0.25 mM DTT, 0.05% Octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.34 Å
6HKT Structure of an H1-bound 6-nucleosome array Deposited 2018-09-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 48 PDB declaration: 50-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain V 1–103（103 aa）
Chain Z 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Chain l 1–103（103 aa）
Chain p 1–103（103 aa）
Chain v 1–103（103 aa）
Chain z 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293.15 K；15% MPD, 0.1 M NaCl and 0.1 M Tris pH 8.8
Resolution 9.70 Å R-free 0.286
6HTS Cryo-EM structure of the human INO80 complex bound to nucleosome Deposited 2018-10-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain J 1–103（103 aa）
Chain N 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IPU Human nucleosome core particle containing 145 bp of DNA Deposited 2018-11-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 17–103（87 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 1.99 Å R-free 0.263
6IQ4 Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups. Deposited 2018-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 17–103（87 aa）
Not recorded AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 4 D0X [Ru(eta(6)-p-cymene)Cl-2(pta) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.25 Å R-free 0.257
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6JOU Crystal structure of the human nucleosome containing H2A.Z.1 S42R Deposited 2019-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.17 Å R-free 0.250
6JR0 Crystal structure of the human nucleosome phased with 12 selenium atoms Deposited 2019-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.50 Å R-free 0.253
6JR1 Crystal structure of the human nucleosome phased with 16 selenium atoms Deposited 2019-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.40 Å R-free 0.243
6JXD Human nucleosome core particle with cohesive end DNA termini Deposited 2019-04-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 17–103（87 aa）
Not recorded MN MANGANESE (II) ION × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.25 Å R-free 0.292
6K1I Human nucleosome core particle with gammaH2A.X variant Deposited 2019-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 23 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；potassium chloride, manganese chloride, potassium cacodylate
Resolution 2.75 Å R-free 0.277
6K1J Human nucleosome core particle with H2A.X variant Deposited 2019-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Potassium Chloride, Manganese Chloride, Potassium Cacodylate
Resolution 2.85 Å R-free 0.319
6K1K Human nucleosome core particle with H2A.X S139E variant Deposited 2019-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 33 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；potassium chloride, manganese chloride, potassium cacodylate
Resolution 2.20 Å R-free 0.275
6KE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.22 Å R-free 0.230
6KVD Crystal structure of human nucleosome containing H2A.J Deposited 2019-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 13 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.21 Å R-free 0.257
6KXV Crystal structure of a nucleosome containing Leishmania histone H3 Deposited 2019-09-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；sodium acetate, isopropanol, manganese chloride, trimethylamine N-oxide
Resolution 3.63 Å R-free 0.264
6L49 H3-CA-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain T 1–103（103 aa）
Chain X 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 18.90 Å
6L4A H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain T 1–103（103 aa）
Chain X 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 12.30 Å
6L9H The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.278
6L9Z 338 bp di-nucleosome assembled with linker histone H1.X Deposited 2019-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CL CHLORIDE ION × 8 CA CALCIUM ION × 65 K POTASSIUM ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate
Resolution 2.50 Å R-free 0.256
6LA2 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 38-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain V 1–103（103 aa）
Chain Z 1–103（103 aa）
Chain f 1–103（103 aa）
Chain j 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, Potassium chloride, Sodium acetate
Resolution 3.89 Å R-free 0.267
6LA8 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 23 K POTASSIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate (cryo-25% MPD)
Resolution 3.40 Å R-free 0.265
6LA9 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 (high cryoprotectant) Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 40 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.70 Å R-free 0.266
6LAB 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0 Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 20 K POTASSIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.20 Å R-free 0.262
6LE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.281
6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CA CALCIUM ION × 6 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.00 Å R-free 0.261
6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 8 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.00 Å R-free 0.261
6M3V 355 bp di-nucleosome harboring cohesive DNA termini Deposited 2020-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded K POTASSIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
Resolution 4.60 Å R-free 0.261
6M44 355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant) Deposited 2020-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
Resolution 3.81 Å R-free 0.286
6M4D Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6M4G Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6M4H Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6MLC PHD6 domain of MLL3 in complex with histone H4 Deposited 2018-09-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain E 2–21（20 aa） Fragment：residues 2-21
Not recorded ZN ZINC ION × 42 GOL GLYCEROL × 6 UNX UNKNOWN LIGAND × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；2 M Na-Form, 0.1 M Tris, pH 8.5
Resolution 1.80 Å R-free 0.216
6MLC PHD6 domain of MLL3 in complex with histone H4 Deposited 2018-09-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain F 2–21（20 aa） Fragment：residues 2-21
Not recorded ZN ZINC ION × 42 GOL GLYCEROL × 24 UNX UNKNOWN LIGAND × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；2 M Na-Form, 0.1 M Tris, pH 8.5
Resolution 1.80 Å R-free 0.216
6MUO CENP-A nucleosome bound by two copies of CENP-C(CD) and one copy CENP-N(NT) Deposited 2018-10-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 9–102（94 aa）
Chain F 9–102（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM HEPES, 50 mN NaCl, 1 mM EDTA, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 8 seconds before plunging
Resolution 3.60 Å
6MUP CENP-A nucleosome bound by two copies of CENP-C(CD) and two copies CENP-N(NT) Deposited 2018-10-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 9–102（94 aa）
Chain F 9–102（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM HEPES, 50 mN NaCl, 1 mM EDTA, 1mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 8 seconds before plunging
Resolution 3.50 Å
6O1D Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA Deposited 2019-02-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；blot for 2.5 sec before plunging
Resolution 3.40 Å
6R0C Human-D02 Nucleosome Core Particle with biotin-streptavidin label Deposited 2019-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6R8Y Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6R8Z Cryo-EM structure of NCP_THF2(-1)-UV-DDB Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6R90 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6R91 Cryo-EM structure of NCP_THF2(-3)-UV-DDB Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6R92 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6R93 Cryo-EM structure of NCP-6-4PP Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6R94 Cryo-EM structure of NCP_THF2(-3) Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6RNY PFV intasome - nucleosome strand transfer complex Deposited 2019-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: octadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE；1 min incubation 3.5s blot
Resolution 3.90 Å
6RXS Crystal structure of CobB Ac3(A76G,Y92A, I131L, V187Y) in complex with H4K16-Acetyl peptide Deposited 2019-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 13–23（11 aa） Fragment：H4K16Ac
Mutation：K16ALY Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350
Resolution 1.60 Å R-free 0.205
6SE0 Class 1 : CENP-A nucleosome Deposited 2019-07-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6SE6 Class2 : CENP-A nucleosome in complex with CENP-C central region Deposited 2019-07-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6SEE Class2A : CENP-A nucleosome in complex with CENP-C central region Deposited 2019-07-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6SEF Class2C : CENP-A nucleosome in complex with CENP-C central region Deposited 2019-07-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6SEG Class1: CENP-A nucleosome in complex with CENP-C central region Deposited 2019-07-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6T79 Structure of a human nucleosome at 3.2 A resolution Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.20 Å
6T7A Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.70 Å
6T7B Structure of human Sox2 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 5.10 Å
6T7C Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.00 Å
6T7D Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.40 Å
6T90 OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2019-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded PTD PENTANEDIAL × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
6T93 Nucleosome with OCT4-SOX2 motif at SHL-6 Deposited 2019-10-25 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.49 Å
6UPK Structure of FACT_subnucleosome complex 1 Deposited 2019-10-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
6UPL Structure of FACT_subnucleosome complex 2 Deposited 2019-10-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.40 Å
6USJ Structure of two nucleosomes bridged by human PARP2 Deposited 2019-10-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Buffer was pH-adjusted and filtered through a 0.22 um filter.
cryo-EM vitrification conditions Cryogen ETHANE；Blot time 2s, blot force 0
Resolution 10.50 Å
6V2K The nucleosome structure after H2A-H2B exchange Deposited 2019-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.60 Å R-free 0.248
6V92 RSC-NCP Deposited 2019-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 33 PDB declaration: 35-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
6VO5 Crystal structure of Human histone acetytransferas 1 (HAT1) in complex with isobutryl-COA and K12A mutant variant of histone H4 Deposited 2020-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–21（20 aa）
Not recorded ACT ACETATE ION × 1 CO6 ISOBUTYRYL-COENZYME A × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；12% PEG 20K and 0.1M MES pH6.5
Resolution 1.60 Å R-free 0.198
6VO5 Crystal structure of Human histone acetytransferas 1 (HAT1) in complex with isobutryl-COA and K12A mutant variant of histone H4 Deposited 2020-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–21（20 aa）
Not recorded CO6 ISOBUTYRYL-COENZYME A × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；12% PEG 20K and 0.1M MES pH6.5
Resolution 1.60 Å R-free 0.198
6X59 The mouse cGAS catalytic domain binding to human assembled nucleosome Deposited 2020-05-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
6X5A The mouse cGAS catalytic domain binding to human nucleosome that purified from HEK293T cells Deposited 2020-05-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.36 Å
6XJD Two mouse cGAS catalytic domain binding to human assembled nucleosome Deposited 2020-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6Y5D Structure of human cGAS (K394E) bound to the nucleosome Deposited 2020-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded PTD PENTANEDIAL × 9 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6Y5E Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex) Deposited 2020-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 23–103（81 aa）
Chain F 21–103（83 aa）
Not recorded PTD PENTANEDIAL × 8 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
6YOV OCT4-SOX2-bound nucleosome - SHL+6 Deposited 2020-04-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
7A08 CryoEM Structure of cGAS Nucleosome complex Deposited 2020-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain e 2–103（102 aa）
Chain i 2–103（102 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
7BWD Structure of Dot1L-H2BK34ub Nucleosome Complex Deposited 2020-04-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.32 Å
7BXT The cryo-EM structure of CENP-A nucleosome in complex with CENP-C peptide and CENP-N N-terminal domain Deposited 2020-04-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7BY0 The cryo-EM structure of CENP-A nucleosome in complex with the phosphorylated CENP-C Deposited 2020-04-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7C0M Human cGAS-nucleosome complex Deposited 2020-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7CIZ Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–103（102 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.
Resolution 1.80 Å R-free 0.214
7CIZ Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.
Resolution 1.80 Å R-free 0.214
7CIZ Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.
Resolution 1.80 Å R-free 0.214
7CJ0 Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 2–103（102 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M Sodium acetate, 0.1 M Tris, pH8.5, 25% (v/v) PEG 4000, 20% (v/v) Glycerol
Resolution 2.50 Å R-free 0.295
7CJ0 Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M Sodium acetate, 0.1 M Tris, pH8.5, 25% (v/v) PEG 4000, 20% (v/v) Glycerol
Resolution 2.50 Å R-free 0.295
7COW 353 bp di-nucleosome harboring cohesive DNA termini with linker histone H1.0 Deposited 2020-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 3 K POTASSIUM ION × 5 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；potassium acetate, calcium chloride, potassium chloride
Resolution 2.86 Å R-free 0.297
7D1Z Cryo-EM structure of SET8-nucleosome complex Deposited 2020-09-15 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7D20 Cryo-EM structure of SET8-CENP-A-nucleosome complex Deposited 2020-09-15 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7DBP Linker histone defines structure and self-association behaviour of the 177 bp human chromosome Deposited 2020-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7E8D NSD2 E1099K mutant bound to nucleosome Deposited 2021-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 3 SFG SINEFUNGIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7EIC Crystal structure of AF9 YEATS domain in complex with H4K5acK8ac peptide Deposited 2021-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–13（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Bis-Tris buffer (pH 6.5) containing 100 mM ammonium acetate and 25% PEG3350
Resolution 1.95 Å R-free 0.205
7JO9 1:1 cGAS-nucleosome complex Deposited 2020-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7JOA 2:1 cGAS-nucleosome complex Deposited 2020-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7JZV Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Deposited 2020-09-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain Q 2–103（102 aa）
Chain q 2–103（102 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7K5X Cryo-EM structure of a chromatosome containing human linker histone H1.0 Deposited 2020-09-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
7K5Y Cryo-EM structure of a chromatosome containing human linker histone H1.4 Deposited 2020-09-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7K60 Cryo-EM structure of a chromatosome containing human linker histone H1.10 Deposited 2020-09-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7K61 Cryo-EM structure of 197bp nucleosome aided by scFv Deposited 2020-09-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
7K63 Cryo-EM structure of a chromatosome containing chimeric linker histone gH1.10-ncH1.4 Deposited 2020-09-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
7LMK Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；13% PEG1500, 20 mM DTT and 200 mM L-proline, 0.1 M HEPES (pH 7.5)
Resolution 2.65 Å R-free 0.258
7LMK Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；13% PEG1500, 20 mM DTT and 200 mM L-proline, 0.1 M HEPES (pH 7.5)
Resolution 2.65 Å R-free 0.258
7LMK Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；13% PEG1500, 20 mM DTT and 200 mM L-proline, 0.1 M HEPES (pH 7.5)
Resolution 2.65 Å R-free 0.258
7LMK Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；13% PEG1500, 20 mM DTT and 200 mM L-proline, 0.1 M HEPES (pH 7.5)
Resolution 2.65 Å R-free 0.258
7LMM Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M MES (pH 6.5) ,13% PEG1500, 20 mM DTT and 200 mM L-proline
Resolution 2.80 Å R-free 0.267
7LMM Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M MES (pH 6.5) ,13% PEG1500, 20 mM DTT and 200 mM L-proline
Resolution 2.80 Å R-free 0.267
7LMM Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M MES (pH 6.5) ,13% PEG1500, 20 mM DTT and 200 mM L-proline
Resolution 2.80 Å R-free 0.267
7LMM Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2 Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 15–27（13 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M MES (pH 6.5) ,13% PEG1500, 20 mM DTT and 200 mM L-proline
Resolution 2.80 Å R-free 0.267
7LYA Cryo-EM structure of the human nucleosome core particle with linked histone proteins H2A and H2B Deposited 2021-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
7LYB Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Deposited 2021-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
7LYC Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Deposited 2021-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
7M98 ATAD2 bromodomain complexed with histone H4K5ac (res 1-10) ligand Deposited 2021-03-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；2.0 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 6.6
Resolution 1.60 Å R-free 0.219
7NL0 Cryo-EM structure of the Lin28B nucleosome core particle Deposited 2021-02-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7PET The 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 36-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Chain l 1–103（103 aa）
Chain p 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
7PEU Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7PEV Nucleosome stack of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7PEW Nucleosome 1 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7PEX Nucleosome 2 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PEY Nucleosome 3 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7PEZ Nucleosome 4 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain l 1–103（103 aa）
Chain p 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
7PF0 Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7PF2 Nucleosome stack of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PF3 Nucleosome 4 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain l 1–103（103 aa）
Chain p 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF4 Nucleosome 3 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF5 Nucleosome 2 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7PF6 Nucleosome 1 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PFA Trinucleosome of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.70 Å
7PFC Nucleosome stack of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
7PFD Nucleosome 1 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFE Nucleosome 2 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFF Nucleosome 3 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7PFT Trinucleosome of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.80 Å
7PFU Nucleosome stack of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
7PFV Nucleosome 1 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFW Nucleosome 2 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.20 Å
7PFX Nucleosome 3 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7PII Structure of the human CCAN CENP-A alpha-satellite complex Deposited 2021-08-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.68 Å
7R5R Structure of the human CCAN CENP-A alpha-satellite complex Deposited 2022-02-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.44 Å
7SCY Nuc147 bound to single BRCT Deposited 2021-09-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7SCZ Nuc147 bound to multiple BRCTs Deposited 2021-09-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7TAN Structure of VRK1 C-terminal tail bound to nucleosome core particle Deposited 2021-12-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.00 Å
7U0G structure of LIN28b nucleosome bound 3 OCT4 Deposited 2022-02-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
7U0I Structure of LIN28b nucleosome bound 2 OCT4 Deposited 2022-02-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
7U0J Structure of 162bp LIN28b nucleosome Deposited 2022-02-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7U46 Cryo-EM structure of CENP-A nucleosome (palindromic alpha satellite DNA) in complex with CENP-N Deposited 2022-02-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.68 Å
7U47 CryoEM structure of CENP-N promoted nucleosome stacks with CENP-A and palindromic alpha satellite DNA sequence Deposited 2022-02-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain M 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.50 Å
7U4D CryoEM structure of CENP-N promoted nucleosome stacks with CENP-A and 601 DNA sequence Deposited 2022-02-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain M 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.10 Å
7U50 APE1 bound to a nucleosome core particle with AP-site at SHL-6 Deposited 2022-03-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7U51 Nucleosome core particle with AP-site at SHL-6 Deposited 2022-03-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7U52 nucleosome core particle with AP-site at SHL-6.5 Deposited 2022-03-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7U53 Nucleosome core particle with AP-site at SHL0 Deposited 2022-03-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7UV9 KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate Deposited 2022-04-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 FE FE (III) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.20 Å
7V1M Structural basis for the co-chaperone relationship of sNASP and ASF1b Deposited 2021-08-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；8% v/v Tacsimate, pH 6.0, 20% w/v PEG 3350
Resolution 2.83 Å R-free 0.240
7V1M Structural basis for the co-chaperone relationship of sNASP and ASF1b Deposited 2021-08-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；8% v/v Tacsimate, pH 6.0, 20% w/v PEG 3350
Resolution 2.83 Å R-free 0.240
7V6Q Crystal structure of sNASP-ASF1A-H3.1-H4 complex Deposited 2021-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 3–103（101 aa）
Not recorded GOL GLYCEROL × 4 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；18% (v/v) Tacsimate, pH 5.0 11% (v/v) PEG2000MME
Resolution 3.00 Å R-free 0.203
7V6Q Crystal structure of sNASP-ASF1A-H3.1-H4 complex Deposited 2021-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 3–103（101 aa）
Not recorded GOL GLYCEROL × 2 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；18% (v/v) Tacsimate, pH 5.0 11% (v/v) PEG2000MME
Resolution 3.00 Å R-free 0.203
7V90 Telomeric mononucleosome Deposited 2021-08-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7V96 Telomeric Dinucleosome Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
7V9C Telomeric Dinucleosome in open state Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7V9J Telomeric trinucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain T 1–103（103 aa）
Chain X 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
7V9K Telomeric tetranucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain T 1–103（103 aa）
Chain X 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.10 Å
7V9S Telomeric trinucleosome in open state Deposited 2021-08-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain T 1–103（103 aa）
Chain X 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7VA4 Telomeric tetranucleosome in open state Deposited 2021-08-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain T 1–103（103 aa）
Chain X 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 14.00 Å
7VCQ structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 Deposited 2021-09-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350
Resolution 3.00 Å R-free 0.283
7VCQ structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 Deposited 2021-09-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350
Resolution 3.00 Å R-free 0.283
7VCQ structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 Deposited 2021-09-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350
Resolution 3.00 Å R-free 0.283
7VZ4 Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA sequence Deposited 2021-11-15 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 1.89 Å
7W9V Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) Deposited 2021-12-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7X57 Cryo-EM structure of human subnucleosome (closed form) Deposited 2022-03-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.63 Å
7X58 Cryo-EM structure of human subnucleosome (open form) Deposited 2022-03-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain D 2–103（102 aa）
Chain F 2–103（102 aa）
Chain H 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain V 1–103（103 aa）
Chain Z 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.51 Å R-free 0.280
7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Chain f 1–103（103 aa）
Chain j 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.51 Å R-free 0.280
7XVM Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 18 CL CHLORIDE ION × 3 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 2.84 Å R-free 0.259
7XX5 Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.19 Å R-free 0.259
7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CA CALCIUM ION × 21 K POTASSIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.39 Å R-free 0.296
7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain V 1–103（103 aa）
Chain Z 1–103（103 aa）
Chain f 1–103（103 aa）
Chain j 1–103（103 aa）
Not recorded CA CALCIUM ION × 26 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.39 Å R-free 0.296
7XZX Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain Deposited 2022-06-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.53 Å
7XZY Cryo-EM structure of the nucleosome containing 193 base-pair DNA with a p53 target sequence Deposited 2022-06-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
7XZZ Cryo-EM structure of the nucleosome in complex with p53 Deposited 2022-06-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7Y00 Cryo-EM structure of the nucleosome containing 169 base-pair DNA with a p53 target sequence Deposited 2022-06-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
7Y5U Cryo-EM structure of the monomeric human CAF1LC-H3-H4 complex Deposited 2022-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7Y5V Cryo-EM structure of the dimeric human CAF1LC-H3-H4 complex Deposited 2022-06-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain E 1–103（103 aa）
Chain J 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.10 Å
7Y5W Cryo-EM structure of the left-handed Di-tetrasome Deposited 2022-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7Y60 Cryo-EM structure of human CAF1LC bound right-handed Di-tetrasome Deposited 2022-06-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7Y61 Cryo-EM structure of the two CAF1LCs bound right-handed Di-tetrasome Deposited 2022-06-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
7Y7I chicken KNL2 in complex with the CENP-A nucleosome Deposited 2022-06-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
7YOZ Cryo-EM structure of human subnucleosome (intermediate form) Deposited 2022-08-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7YWX Structure of the human CCAN CENP-A alpha-satellite complex Deposited 2022-02-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 12.00 Å
7YYH Structure of the human CCANdeltaT CENP-A alpha-satellite complex Deposited 2022-02-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.90 Å
7ZI4 Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Deposited 2022-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain J 1–103（103 aa）
Chain N 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；4uL of sample applied to Quantifoil R2/2 Cu 300 mesh grids. blot parameters were wait time 30 sec, blot time 0.5 sec, blot force -8
Resolution 3.20 Å
8AAG H1-bound palindromic nucleosome, state 1 Deposited 2022-07-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 10.00 Å
8ATF Nucleosome-bound Ino80 ATPase Deposited 2022-08-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8AV6 CryoEM structure of INO80 core nucleosome complex in closed grappler conformation Deposited 2022-08-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.68 Å
8DK5 Structure of 187bp LIN28b nucleosome with site 0 mutation Deposited 2022-07-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8EVG 162bp CX3CR1 nucleosome (further classified with better nucleosome end) Deposited 2022-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
8EVH CX3CR1 nucleosome and wild type PU.1 complex Deposited 2022-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
8EVI CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations Deposited 2022-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8EVJ CX3CR1 nucleosome bound PU.1 and C/EBPa Deposited 2022-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8GUI Bre1-nucleosome complex (Model I) Deposited 2022-09-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
8GUJ Bre1-nucleosome complex (Model II) Deposited 2022-09-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8GUK Human nucleosome core particle (free form) Deposited 2022-09-12 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.51 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8H1T Cryo-EM structure of BAP1-ASXL1 bound to chromatosome Deposited 2022-10-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8HLW Crystal structure of SIRT3 in complex with H4K16la peptide Deposited 2022-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 14–21（8 aa） Fragment：residues 20-27, with lactylated No.23 lysine
Not recorded ZN ZINC ION × 1 2OP (2S)-2-HYDROXYPROPANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；0.1 M Tris pH 8.5, 25% (w/v) Polyethylene glycol 3350
Resolution 2.50 Å R-free 0.243
8IEG Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deposited 2023-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain F 23–102（80 aa）
Chain L 23–102（80 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8IEJ RNF20-RNF40/hRad6A-Ub/nucleosome complex Deposited 2023-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain F 23–102（80 aa）
Chain L 23–102（80 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
8IHL Overlapping tri-nucleosome Deposited 2023-02-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Chain V 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.64 Å
8IQF Cryo-EM structure of the dimeric human CAF1-H3-H4 complex Deposited 2023-03-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain E 1–103（103 aa）
Chain J 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8IQG Cryo-EM structure of the monomeric human CAF1-H3-H4 complex Deposited 2023-03-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8J6S Cryo-EM structure of the single CAF-1 bound right-handed Di-tetrasome Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8J6T Cryo-EM structure of the double CAF-1 bound right-handed Di-tetrasome Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
8JBX Human canonical 601 DNA nucleosome Deposited 2023-05-09 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
8JCC Human histone H2B variant H2BFWT Cryo-EM structure with 601 DNA sequence Deposited 2023-05-10 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
8JCD Human H2BFWTH100R nucleosome with 601 DNA Deposited 2023-05-11 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8JHF Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 18–103（86 aa）
Chain F 18–103（86 aa）
Mutation：K20M Mutation：K20M ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.68 Å
8JHG Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 18–103（86 aa）
Chain F 18–103（86 aa）
Mutation：K20M Mutation：K20M ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.58 Å
8JL9 Cryo-EM structure of the human nucleosome with scFv Deposited 2023-06-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
8JLA Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 Deposited 2023-06-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8JLB Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant Deposited 2023-06-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
8JLD Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail Deposited 2023-06-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
8JND The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-06-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 19-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
8JNE The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding Deposited 2023-06-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.68 Å
8JNF The cryo-EM structure of the RAD51 filament bound to the nucleosome Deposited 2023-06-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.91 Å
8KB5 Cryo-EM structure of the human nucleosome containing H3.8 Deposited 2023-08-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.26 Å
8KCY Structure of nucleosome complexed with two DEK molecules Deposited 2023-08-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8KD1 Structure of nucleosome complexed with one DEK molecule Deposited 2023-08-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8KE0 Structure of H1.2 bound to the nucleosome Deposited 2023-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8OFF Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes (Map1) Deposited 2023-03-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain Da 1–103（103 aa）
Chain Db 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；blot force = 0 N blot time = 8 s
Resolution 3.40 Å
8OL1 cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure) Deposited 2023-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 23–103（81 aa）
Chain F 23–103（81 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；PBS buffer
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8OO7 CryoEM Structure INO80core Hexasome complex composite model state1 Deposited 2023-04-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
Resolution 2.80 Å
8OOA CryoEM Structure INO80core Hexasome complex Hexasome refinement state1 Deposited 2023-04-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
Resolution 3.18 Å
8OOP CryoEM Structure INO80core Hexasome complex composite model state2 Deposited 2023-04-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 2 ALF TETRAFLUOROALUMINATE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
Resolution 2.70 Å
8OOS CryoEM Structure INO80core Hexasome complex ATPase-hexasome refinement state 2 Deposited 2023-04-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ALF TETRAFLUOROALUMINATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
Resolution 3.29 Å
8OSJ Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Deposited 2023-04-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
8OSK Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) Deposited 2023-04-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8OSL Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement) Deposited 2023-04-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
8OTS OCT4 and MYC-MAX co-bound to a nucleosome Deposited 2023-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8OTT MYC-MAX bound to a nucleosome at SHL+5.8 Deposited 2023-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 22–103（82 aa）
Chain F 22–103（82 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8OX0 Structure of apo telomeric nucleosome Deposited 2023-04-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25 mM HEPES-KOH pH 8.0, 150 mM KCl, 1 mM MgCl2, 1% glycerol, 0.01% Igepal CA-630,1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Blot Force: -15 Blot Time: 2.5 s
Resolution 2.52 Å
8OX1 Structure of TRF1core in complex with telomeric nucleosome Deposited 2023-04-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；25 mM HEPES-KOH pH 8.0, 150 mM KCl, 1 mM MgCl2, 1% glycerol, 0.01% Igepal CA-630, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE；Blot Force: -15 Blot Time: 2.5 s
Resolution 2.70 Å
8PEF Crystal structure of SLF1 Ankyrin repeat domain in complex with H4 tail (K20me0) Deposited 2023-06-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 10–26（17 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1M Sodium malonate dibasic monohydrate 0.1M Hepes pH 7 30% (w/v) Poly(acrylic acid sodium salt) 2100
Resolution 1.28 Å R-free 0.225
8Q36 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound) Deposited 2023-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain BBB 17–103（87 aa）
Chain FFF 17–103（87 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0].
Resolution 2.60 Å R-free 0.262
8Q3E High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain BBB 17–103（87 aa）
Chain FFF 17–103（87 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.17 Å R-free 0.270
8Q3M Structure of Nucleosome Core with a Bound Kaposi Sarcoma Associated Herpesvirus LANA Peptide Having a Methionine to Ornithine Substitution Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain BBB 17–103（87 aa）
Chain FFF 17–103（87 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.50 Å R-free 0.268
8Q3X Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound) Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain BBB 17–103（87 aa）
Chain FFF 17–103（87 aa）
Not recorded AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.30 Å R-free 0.262
8QZM Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome Deposited 2023-10-27 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5, 65 mM NaCl, 1 mM DTT, 0.1 mM S-Adenosyl methionine
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8RBX Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex Deposited 2023-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 43 PDB declaration: 46-meric
Chain O 1–103（103 aa）
Chain U 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8RGM Cryo-EM structure of nucleosome containing Widom603 DNA Deposited 2023-12-14 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8SB6 Structure of human BRD2-BD1 bound to a histone H4 acetyl-methyllysine peptide Deposited 2023-04-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–16（15 aa） Fragment：N-terminal peptide (UNP residues 2-16)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES, pH 6.7, 20-25% PEG5000 MME, 0.2 M ammonium sulfate
Resolution 1.80 Å R-free 0.204
8SB6 Structure of human BRD2-BD1 bound to a histone H4 acetyl-methyllysine peptide Deposited 2023-04-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2–16（15 aa） Fragment：N-terminal peptide (UNP residues 2-16)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES, pH 6.7, 20-25% PEG5000 MME, 0.2 M ammonium sulfate
Resolution 1.80 Å R-free 0.204
8SMW Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SMX Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMY Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMZ Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN0 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN1 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SN2 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8SPS High resolution structure of ESRRB nucleosome bound OCT4 at site a and site b Deposited 2023-05-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8SPU Structure of ESRRB nucleosome bound OCT4 at site c Deposited 2023-05-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8SYP Genomic CX3CR1 nucleosome Deposited 2023-05-25 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8TGP Crystal structure of SIRT2 with FAM-PEG4-H4K16(myristoyl) peptide Deposited 2023-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 9–21（13 aa）
Not recorded ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M MES monohydrate pH 6.5 (NaOH), 20% w/v PEG 4,000
Resolution 1.76 Å R-free 0.230
8TXV Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Deposited 2023-08-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TXW Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Deposited 2023-08-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TXX Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Deposited 2023-08-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8U13 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) Deposited 2023-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8U14 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Deposited 2023-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8U9S Cryo-EM structure of NRCAM nucleosome aided by scFv Deposited 2023-09-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8UBJ Cryo-EM structure of NRCAM nucleosome aided by scFv (3D Flex map) Deposited 2023-09-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8UBK Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome Deposited 2023-09-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8UBL Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome (3D Flex map) Deposited 2023-09-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8UPF Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Deposited 2023-10-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8VFX Cryo-EM structure of 186bp ALBN1 nucleosome aided by scFv Deposited 2023-12-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
8VFY Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1) Deposited 2023-12-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
8VFZ Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2) Deposited 2023-12-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8VG0 Cryo-EM structure of GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8VG1 Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
8VG2 Cryo-EM structure of FoxA1 and GATA4 in complex with H14 chromatosome Deposited 2023-12-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8VLR Cryo-EM structure of native H2AK119bu nucleosome at 2.6 Deposited 2024-01-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 20–103（84 aa）
Chain F 20–103（84 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Tris-HCl, pH 7.5, 50 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8VMJ H3K4me3 nucleosome bound to PRC2_AJ119-450 Deposited 2024-01-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain J 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VMN H3K4me3 nucleosome bound to PRC2_AJ1-450 Deposited 2024-01-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain J 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8VO0 H3K36me3-modified nucleosome bound to PRC2_AJ1-450 with histone H3 tail disengaged Deposited 2024-01-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain J 26–103（78 aa）
Chain Q 25–103（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8VOB H3K36me3-modified nucleosome bound to PRC2_AJ1-450 Deposited 2024-01-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain J 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VWS Nucleosome containing 8oxoG at SHL-6 Deposited 2024-02-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VWT OGG1 bound to a nucleosome containing 8oxoG at SHL-6 (composite map) Deposited 2024-02-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8VWU Nucleosome containing 8oxoG at SHL4 Deposited 2024-02-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8VWV OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map) Deposited 2024-02-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8W9D Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8W9E Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8W9F Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 24–102（79 aa）
Chain F 24–102（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8X15 Structure of nucleosome-bound SRCAP-C in the apo state Deposited 2023-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain D 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8X19 Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state Deposited 2023-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain D 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8X1C Structure of nucleosome-bound SRCAP-C in the ADP-bound state Deposited 2023-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric
Chain D 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8X7I Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Deposited 2023-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 20–102（83 aa）
Chain F 20–102（83 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8X7J Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Deposited 2023-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 21–102（82 aa）
Chain F 21–102（82 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8X7K Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) Deposited 2023-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 21–102（82 aa）
Chain F 21–102（82 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8XBT The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.12 Å
8XBU The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.24 Å
8XBW The cryo-EM structure of the RAD51 N-terminal lobe domain bound to the histone H4 tail of the nucleosome Deposited 2023-12-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8Y3C Cryo-EM structure of the overlapping di-nucleosome (closed form) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.21 Å
8Y3D Cryo-EM structure of the overlapping di-nucleosome (intermediate form2) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
8Y3E Cryo-EM structure of the overlapping di-nucleosome (open form) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.32 Å
8Y3F Cryo-EM structure of the overlapping di-nucleosome (intermediate form1) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.54 Å
8YBJ Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence Deposited 2024-02-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.38 Å
8YBK Cryo-EM structure of the human nucleosome containing the H3.1 E97K mutant Deposited 2024-02-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.69 Å
8YE8 Crystal structure of mouse BAHCC1 TTD domain in complex with H4K20me1 peptide Deposited 2024-02-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 15–26（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM MES, pH 6.5, 10 mM Li2SO4, 8% PEG20000 and 3 mM H4K20me
Resolution 1.90 Å R-free 0.238
8YJF Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and an H2A-H2B dimer Deposited 2024-03-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M calcium acetate, 0.1 M Sodium cacodylate pH 5.5, 12% (w/v) PEG 8000
Resolution 4.40 Å R-free 0.312
8YJM Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and a single chain H2B-H2A chimera Deposited 2024-03-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.2 M sodium acetate, 0.1 M sodium citrate pH 5.5, 5%(w/v) PEG 4000
Resolution 4.15 Å R-free 0.286
8YNY Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome Deposited 2024-03-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: 13-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.52 Å
8YTI Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2024-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded CL CHLORIDE ION × 8 CA CALCIUM ION × 52 K POTASSIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45 mM CaCl2, 25 mM KCl, 10 mM Na-acetate (pH 4.5)
Resolution 2.70 Å R-free 0.267
8YV8 Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence. Deposited 2024-03-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8Z50 Crystal structure of the ASF1-H3T-H4 complex Deposited 2024-04-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.0 M Lithium chloride, 0.1 M MES pH 6.0, 10% PEG 6000
Resolution 2.80 Å R-free 0.255
8ZJR Structure of nucleosome-bound RFX5 complex Deposited 2024-05-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8ZJT Structure of free nucleosome Deposited 2024-05-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9BE6 Cryo-EM structure of Human Nucleosome collected by Leginon on Krios at 3.0 Angstrom resolution Deposited 2024-04-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain F 26–103（78 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9D3K Two Dsup molecules in complex with the nucleosome open from both sides Deposited 2024-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 24–102（79 aa）
Chain F 24–102（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9D3L Two Dsup molecules in complex with the nucleosome open from the left side Deposited 2024-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 24–102（79 aa）
Chain F 24–102（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9D3M Two HMGN2s in complex with the nucleosome Deposited 2024-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 22–103（82 aa）
Chain F 22–103（82 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9D3N 167-bp 5S rDNA nucleosome cross-linked with glutaraldehyde Deposited 2024-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 25–103（79 aa）
Chain F 25–103（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9D3O 167-bp 5S rDNA nucleosome - closed Deposited 2024-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 22–103（82 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9D3P 167-bp 5S rDNA nucleosome - open I (open only on the downstream side) Deposited 2024-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 22–103（82 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9D3Q 167-bp 5S rDNA nucleosome - open II Deposited 2024-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 23–103（81 aa）
Chain F 23–103（81 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9D3R 147-bp 5S rDNA nucleosome - closed Deposited 2024-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 22–103（82 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9D3S 147-bp 5S rDNA nucleosome - open I (open on the downstream side) Deposited 2024-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 22–103（82 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9D3T 147-bp 5S rDNA nucleosome cross-linked with glutaraldehyde Deposited 2024-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 25–102（78 aa）
Chain F 25–102（78 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9DWF Nucleosome containing a 1-nt gap at SHL-4.5 Deposited 2024-10-09 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9DWG DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 1, composite) Deposited 2024-10-09 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9DWH DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 2, composite) Deposited 2024-10-09 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9DWI DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 3, composite) Deposited 2024-10-09 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9DWJ Nucleosome containing a 1-nt gap at SHL-3.5 Deposited 2024-10-09 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9DWK DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-3.5 Deposited 2024-10-09 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9DWL Nucleosome containing a 1-nt gap at SHL-5.5 Deposited 2024-10-09 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9DWM DNA polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5 Deposited 2024-10-09 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1；25mM HEPES (pH-7.1), 50mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9E00 Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.75 Å
9E05 The consensus model of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
9E09 Cryo-EM structure a single nucleosome (2) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.72 Å
9E0R Cryo-EM structure of a single nucleosome (1) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9E2D Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome with a five base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.08 Å
9E2F Cryo-EM structure of a di-nucleosome with a five base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
9E2Q Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with a six base pair linker Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
9E2R Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome and an histone-3 peptide Deposited 2024-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.71 Å
9E3D Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with K120R mutant H2B Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9E3R Cryo-EM structure of PWWP domain deleted DNMT 3A2/3B3 in complex with a di-nucleosome Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
9E3U Cryo-EM structure of DNMT 3A2/3B3 tetramer bound to a di-nucleosome with a 25 base-pair linker Deposited 2024-10-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
9E49 Cryo-EM structure of a di-nucleosome with an eight base-pair linker Deposited 2024-10-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.93 Å
9ECP Structure of the native human NCP purified from HEK293 cells Deposited 2024-11-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 22–103（82 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.91 Å
9EOZ Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0 Deposited 2024-03-16 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9FGQ Structure of human APC3loop 375-381 bound to the NCP Deposited 2024-05-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPEs pH8.0, 50 mM NaCl, 0.5 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9FH9 Structure of CyclinB1 N-terminus bound to the NCP Deposited 2024-05-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9GCG CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Deposited 2024-08-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å
9GE4 CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Deposited 2024-08-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
9GE5 CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain N 23–103（81 aa）
Chain R 26–103（78 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
9GEL CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.86 Å
9GEV CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9GF6 CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9GFB CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
9GFM CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain N 22–103（82 aa）
Chain R 25–103（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9GMK SIRT7:H3K18DTU nucleosome complex Deposited 2024-08-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9GMR SIRT7-H3K36MTUnucleosome complex Deposited 2024-08-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded A1IY0 [[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-2-(methylamino)-6-oxidanyl-2-(propylamino)-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9GW2 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Deposited 2024-09-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.84 Å
9GXA CENP-A/H4 di-tetrasome assembled on alpha-satellite DNA. Deposited 2024-09-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain D 2–103（102 aa）
Chain F 2–103（102 aa）
Chain H 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.01 Å
9IGW Ku70/80 bound to 147 bp nucleosome Deposited 2025-02-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
9IGX Ku70/80 bound to 153 bp nucleosome Deposited 2025-02-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 18–101（84 aa）
Chain F 18–101（84 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å
9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9IPU cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Deposited 2024-07-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9J0N Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 27 PDB declaration: 30-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9J0O Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9J0P Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9J8M Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (High mobility complex) Deposited 2024-08-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.82 Å
9J8N Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (Low mobility complex) Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 32-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.14 Å
9J8O Cryo-EM structure of BAF-Lamin A/C IgF-H1-nucleosome complex Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 28-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
9J8W Cryo-EM structure of NCP-UV-DDB complex containing CPD Deposited 2024-08-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
9JC6 Human H2BW2 nucleosome Deposited 2024-08-28 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
9K9L Cryo-EM structure of the human CENP-A-H4 octasome. Deposited 2024-10-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain D 1–103（103 aa）
Chain F 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9KQO cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome Deposited 2024-11-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain F 2–103（102 aa）
Chain L 2–103（102 aa）
Not recorded ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9L1X hDEK-nucleosome complex (conformation 1) Deposited 2024-12-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded UNX UNKNOWN LIGAND × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
9L22 hDEK-nucleosome complex (conformation 2) Deposited 2024-12-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded UNX UNKNOWN LIGAND × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9MLL GammaH2AX containing nucleosomes, Parallel stack Deposited 2024-12-19 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain M 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9MLN GammaH2AX containing nucleosome, Canonical (Class 1) Deposited 2024-12-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9MLR GammaH2AX containing nucleosome, Half-wrapped (Class 2) Deposited 2024-12-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9MLS GammaH2AX containing nucleosome, Extended (Class 3) Deposited 2024-12-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9MMK H2AX containing nucleosome, Canonical (Class 1) Deposited 2024-12-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9MMM H2AX containing nucleosomes, Parallel stack Deposited 2024-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain M 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9MMN H2AX containing nucleosomes, Left offset stack Deposited 2024-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain M 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9MMO H2AX containing nucleosomes, Right offset stack Deposited 2024-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain M 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9MMT H2AX containing nucleosome, Unwrapped (Class 2) Deposited 2024-12-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9NQU KDM6B-nucleosome structure stabilized by H3K27C-UNC8015 covalent conjugate Deposited 2025-03-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded FE FE (III) ION × 1 ZN ZINC ION × 1 OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.16 Å
9OGR Cryo-EM analysis of human H2A.Z on methylated Sat2R-P DNA (v1) Deposited 2025-05-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9OGS Cryo-EM analysis of human H2A.Z on Sat2R-P DNA (v1) Deposited 2025-05-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9OGZ Cryo-EM analysis of human H2A.Z on Sat2R-P DNA (v2) Deposited 2025-05-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9OH0 Cryo-EM analysis of human H2A.Z on methylated Sat2R-P DNA (v2) Deposited 2025-05-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9OH1 Cryo-EM analysis of human H2A.Z on 601L DNA Deposited 2025-05-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
9OH2 Cryo-EM analysis of human H2A.Z on methylated 601L DNA Deposited 2025-05-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
9Q80 Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome Deposited 2025-02-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9Q8X Ku70/80 bound to a 153 bp H2AX nucleosome Deposited 2025-02-25 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
9Q9F DNA-PK bound to a 153 bp H2AX nucleosome model 1 Deposited 2025-02-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.54 Å
9QCR DNA-PK bound to 153 bp H2AX nucleosome model 2 Deposited 2025-03-05 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.37 Å
9QCS Ku80 mediated DNA-PK dimer bound to 153 bp H2AX nucleosome Deposited 2025-03-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
9QMS DNA-PK bound to 153 bp H2AX nucleosome with ATPyS Deposited 2025-03-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 30-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
9R04 p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample) Deposited 2025-04-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9R2M p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, composite map) Deposited 2025-04-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9R2P p53 bound to nucleosome at position SHL+5.9 (crosslinked sample) Deposited 2025-04-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
9R2Q p53 bound to nucleosome at position SHL-5.7 (non-crosslinked sample) Deposited 2025-04-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9RL4 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2025-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded PTD PENTANEDIAL × 16 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9RMC Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1 Deposited 2025-06-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9RN1 Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2 Deposited 2025-06-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
9RN2 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 Deposited 2025-06-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
9RZC State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Deposited 2025-07-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9RZE State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Deposited 2025-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.53 Å
9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
9TAX Structure of the human inner kinetochore CCAN bound to a mono-CENP-A nucleosome Deposited 2025-11-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain d 1–103（103 aa）
Chain h 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
9TAY Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome Deposited 2025-11-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 37-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain d 1–103（103 aa）
Chain h 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.50 Å
9U5U The 1:1 cryo-EM structure of BAP1/ASXL1-K351Ub in complex with H2AK119Ub nucleosome Deposited 2025-03-21 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain b 1–103（103 aa）
Chain d 1–103（103 aa）
Chain f 1–103（103 aa）
Chain h 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain f 1–103（103 aa）
Chain h 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.54 Å
9UZ7 Cryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking Deposited 2025-05-16 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–103（102 aa）
Chain D 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；10 mM HEPES, pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution not provided
9V6Q Cryo-EM structure of two cPRC1 complexes bound to opposite faces of an endogenous 147-bp mono-nucleosome Deposited 2025-05-27 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.60 Å
9V6S Cryo-EM structure of a single cPRC1 complex engaged on one face of an endogenous 147-bp mononucleosome Deposited 2025-05-27 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
9V6X Cryo-EM structure of the cPRC1 complex bound to an endogenous 184-bp mono-nucleosome Deposited 2025-05-27 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.00 Å
9V8L Cryo-EM structure of the cPRC1-di-nucleosome (loose) complex Deposited 2025-05-29 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain S 1–103（103 aa）
Chain T 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 6.60 Å
9V9H Cryo-EM structure of the cPRC1-di-nucleosome (tight) complex Deposited 2025-05-30 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain Q 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.50 Å
9V9P Cryo-EM structure of the cPRC1-di-nucleosome (CBX7) complex Deposited 2025-06-01 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain Q 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.40 Å
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9XSF Cryo-EM structure of H4S47GlcNAc nucleosome at 3.39 angstrom Deposited 2025-11-20 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.39 Å
9Y46 Human nucleosome structure on Nickel-NTA lipid affinity grid (C2 refinement) Deposited 2025-09-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.59 Å
9Y47 Human nucleosome structure on Nickel-NTA lipid affinity grid (C1 refinement) Deposited 2025-09-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.74 Å
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å
9ZEN Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2 Deposited 2025-11-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 25–103（79 aa）
Chain F 25–103（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
9ZEO Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1 Deposited 2025-11-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 21–103（83 aa）
Chain F 21–103（83 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

581 other PDB entries and 633 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H4_HUMAN
Isoform —
PDB entities 6
Chains and sequence ranges Author chain B； PDBConstruct 1–102； UniProt 2–103 Author chain F； PDBConstruct 1–102； UniProt 2–103

Histone H2A type 1-B/E

Homo sapiens

UniProt P04908

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 15 DNA 2 PDB declaration: 17-meric（17） Consistent with all polymer counts Chain C； UniProt 2–130 Chain G； UniProt 2–130 Not recorded Ubiquitin × 1 （P0CG47） [histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D × 1 （A0A6P6IDI8,O14686） Retinoblastoma-binding protein 5 × 1 （Q15291） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2B type 2-E × 2 （Q16778） DNA (145-MER) × 1 WD repeat-containing protein 5 × 1 （P61964） DNA (145-MER) × 1 Protein dpy-30 homolog × 2 （Q9C005） ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.63 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9YLE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2RVQ Solution structure of the isolated histone H2A-H2B heterodimer Deposited 2016-03-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–130（130 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；293 K；Ionic strength (raw mmCIF value) 400；Pressure ambient
NMR sample composition 0.1-0.3 mM [U-13C; U-15N; U-2H] entity_1-1, 0.1-0.3 mM [U-13C; U-15N; U-2H] entity_2-2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3A6N The nucleosome containing a testis-specific histone variant, human H3T Deposited 2009-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.264
3AFA The human nucleosome structure Deposited 2010-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.270
3AN2 The structure of the centromeric nucleosome containing CENP-A Deposited 2010-08-27 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.60 Å R-free 0.325
3AV1 The human nucleosome structure containing the histone variant H3.2 Deposited 2011-02-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.290
3AV2 The human nucleosome structure containing the histone variant H3.3 Deposited 2011-02-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.272
3AYW Crystal Structure of Human Nucleosome Core Particle Containing H3K56Q mutation Deposited 2011-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.90 Å R-free 0.273
3AZE Crystal Structure of Human Nucleosome Core Particle Containing H3K64Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.302
3AZF Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.263
3AZG Crystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.40 Å R-free 0.269
3AZH Crystal Structure of Human Nucleosome Core Particle Containing H3K122Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.49 Å R-free 0.266
3AZI Crystal Structure of Human Nucleosome Core Particle Containing H4K31Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.289
3AZJ Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.89 Å R-free 0.268
3AZK Crystal Structure of Human Nucleosome Core Particle Containing H4K59Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.20 Å R-free 0.258
3AZL Crystal Structure of Human Nucleosome Core Particle Containing H4K77Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.259
3AZM Crystal Structure of Human Nucleosome Core Particle Containing H4K79Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.89 Å R-free 0.296
3AZN Crystal Structure of Human Nucleosome Core Particle Containing H4K91Q mutation Deposited 2011-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.254
3W96 Crystal Structure of Human Nucleosome Core Particle lacking H2A N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 11–130（120 aa） Fragment：UNP residues 11-130
Chain G 11–130（120 aa） Fragment：UNP residues 11-130
Not recorded CL CHLORIDE ION × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.296
3W97 Crystal Structure of Human Nucleosome Core Particle lacking H2B N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.20 Å R-free 0.321
3W98 Crystal Structure of Human Nucleosome Core Particle lacking H3.1 N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.42 Å R-free 0.303
3W99 Crystal Structure of Human Nucleosome Core Particle lacking H4 N-terminal region Deposited 2013-04-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.312
3WKJ The nucleosome containing human TSH2B Deposited 2013-10-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.291
3WTP Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3 Deposited 2014-04-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, vapor diffusion, hanging drop, temperature 293K
Resolution 2.67 Å R-free 0.270
3X1S Crystal structure of the nucleosome core particle Deposited 2014-11-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70mM KCL, 70-90mM MnCl2, 24% MPD, 20mM Na-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.81 Å R-free 0.270
3X1V Crystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming Deposited 2014-11-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MN MANGANESE (II) ION × 19 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70 mM KCl, 70-90 mM MnCl2, Na-cocodylate, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.92 Å R-free 0.259
4YM5 Crystal structure of the human nucleosome containing 6-4PP (inside) Deposited 2015-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 4.00 Å R-free 0.289
4YM6 Crystal structure of the human nucleosome containing 6-4PP (outside) Deposited 2015-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.51 Å R-free 0.287
4Z5T The nucleosome containing human H3.5 Deposited 2015-04-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.80 Å R-free 0.269
5AV5 human nucleosome core particle Deposited 2015-06-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions LIQUID DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.233
5AV6 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.229
5AV8 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.233
5AV9 human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.20 Å R-free 0.239
5AVB human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.236
5AVC human nucleosome core particle Deposited 2015-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.40 Å R-free 0.238
5AY8 Crystal structure of human nucleosome containing H3.Y Deposited 2015-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；sodium acetate, manganese chloride, 2-propanol, trimethylamine N-oxide
Resolution 2.80 Å R-free 0.249
5B0Y Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122 Deposited 2015-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.56 Å R-free 0.249
5B0Z The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution Deposited 2015-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 1.99 Å R-free 0.254
5B24 The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer Deposited 2015-12-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.60 Å R-free 0.249
5B2I Human nucleosome containing CpG unmethylated DNA Deposited 2016-01-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 3.00 Å R-free 0.257
5B2J Human nucleosome containing CpG methylated DNA Deposited 2016-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
Resolution 2.60 Å R-free 0.252
5B31 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1. Deposited 2016-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.20 Å R-free 0.271
5B32 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3. Deposited 2016-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.35 Å R-free 0.259
5B40 The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations Deposited 2016-03-22 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；90mM Tris-HCl (pH 7.8), 3.6% PGA-LM, 25.2% PEG 400, 2-6% Pentaerythritol ethoxylate (3/4 EO/OH)
Resolution 3.33 Å R-free 0.263
5CPI Nucleosome containing unmethylated Sat2R DNA Deposited 2015-07-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.90 Å R-free 0.295
5CPJ Nucleosome containing methylated Sat2R DNA Deposited 2015-07-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 3.15 Å R-free 0.295
5CPK Nucleosome containing methylated Sat2L DNA Deposited 2015-07-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.63 Å R-free 0.284
5GSE Crystal structure of unusual nucleosome Deposited 2016-08-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；potassium bromide, potassium thiocyanate, Tris-HCl, PGA-LM, PEG 400
Resolution 3.14 Å R-free 0.255
5GTC Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle Deposited 2016-08-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.70 Å R-free 0.267
5GXQ The crystal structure of the nucleosome containing H3.6 Deposited 2016-09-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.85 Å R-free 0.262
5JRG Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF) Deposited 2016-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.50 Å R-free 0.245
5VEY Solution NMR structure of histone H2A-H2B mono-ubiquitylated at H2A Lys15 in complex with RNF169 (653-708) Deposited 2017-04-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 13–106（94 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50 mM KCl；Pressure 1
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
NMR sample composition 90% H2O/10% D2O
Resolution not provided
5X7X The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution Deposited 2017-02-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.18 Å R-free 0.256
5XF3 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RRK (1R,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
Resolution 2.60 Å R-free 0.270
5XF4 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (S,S-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 SSK (1S,2S)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
Resolution 2.87 Å R-free 0.266
5XF5 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,S-configuration) Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RSK (1S,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；35-55mM MnCl2, 25-49mM KCl, 20mM K-Cacodylate pH 6.0
Resolution 2.82 Å R-free 0.264
5Y0C Crystal Structure of the human nucleosome at 2.09 angstrom resolution Deposited 2017-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MN MANGANESE (II) ION × 10 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.09 Å R-free 0.249
5Y0D Crystal Structure of the human nucleosome containing the H2B E76K mutant Deposited 2017-07-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 1.99 Å R-free 0.252
5Z23 Crystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD Deposited 2017-12-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：L51M,L58M,L93M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L51M,L58M,L93M Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.73 Å R-free 0.261
5ZBX The crystal structure of the nucleosome containing histone H3.1 CATD(V76Q, K77D) Deposited 2018-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.58 Å R-free 0.249
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6BUZ Cryo-EM structure of CENP-A nucleosome in complex with kinetochore protein CENP-N Deposited 2017-12-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
6E0C Cryo-EM structure of the CENP-A nucleosome (W601) in complex with a single chain antibody fragment Deposited 2018-07-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.63 Å
6E0P Cryo-EM structure of the centromeric nucleosome (Native alpha satellite DNA) in complex with a single chain antibody fragment Deposited 2018-07-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；blot for 2.5 sec before plunging
Resolution 2.60 Å
6HKT Structure of an H1-bound 6-nucleosome array Deposited 2018-09-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 48 PDB declaration: 50-meric
Chain 0 1–130（130 aa）
Chain 2 1–130（130 aa）
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain W 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Chain m 1–130（130 aa）
Chain q 1–130（130 aa）
Chain w 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293.15 K；15% MPD, 0.1 M NaCl and 0.1 M Tris pH 8.8
Resolution 9.70 Å R-free 0.286
6HTS Cryo-EM structure of the human INO80 complex bound to nucleosome Deposited 2018-10-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain K 1–130（130 aa）
Chain O 1–130（130 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IPU Human nucleosome core particle containing 145 bp of DNA Deposited 2018-11-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 14–120（107 aa）
Chain G 14–120（107 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 1.99 Å R-free 0.263
6IQ4 Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups. Deposited 2018-11-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–120（106 aa）
Chain G 15–120（106 aa）
Not recorded AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 4 D0X [Ru(eta(6)-p-cymene)Cl-2(pta) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.25 Å R-free 0.257
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6JR0 Crystal structure of the human nucleosome phased with 12 selenium atoms Deposited 2019-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：L65M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L65M Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.50 Å R-free 0.253
6JR1 Crystal structure of the human nucleosome phased with 16 selenium atoms Deposited 2019-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：L65M, L85M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L65M, L85M Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.40 Å R-free 0.243
6JXD Human nucleosome core particle with cohesive end DNA termini Deposited 2019-04-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 14–119（106 aa）
Chain G 14–119（106 aa）
Not recorded MN MANGANESE (II) ION × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.25 Å R-free 0.292
6KE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–119（105 aa）
Chain G 15–119（105 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.22 Å R-free 0.230
6KXV Crystal structure of a nucleosome containing Leishmania histone H3 Deposited 2019-09-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；sodium acetate, isopropanol, manganese chloride, trimethylamine N-oxide
Resolution 3.63 Å R-free 0.264
6L49 H3-CA-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 18.90 Å
6L4A H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 12.30 Å
6L9H The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–119（105 aa）
Chain G 15–119（105 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.278
6L9Z 338 bp di-nucleosome assembled with linker histone H1.X Deposited 2019-11-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CL CHLORIDE ION × 8 CA CALCIUM ION × 65 K POTASSIUM ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate
Resolution 2.50 Å R-free 0.256
6LA2 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 38-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain W 1–130（130 aa）
Chain a 1–130（130 aa）
Chain g 1–130（130 aa）
Chain k 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, Potassium chloride, Sodium acetate
Resolution 3.89 Å R-free 0.267
6LA8 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 23 K POTASSIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate (cryo-25% MPD)
Resolution 3.40 Å R-free 0.265
6LA9 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 (high cryoprotectant) Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 40 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.70 Å R-free 0.266
6LAB 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0 Deposited 2019-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 20 K POTASSIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.20 Å R-free 0.262
6LE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–119（105 aa）
Chain G 15–119（105 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
Resolution 2.60 Å R-free 0.281
6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded CA CALCIUM ION × 6 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.00 Å R-free 0.261
6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 8 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
Resolution 3.00 Å R-free 0.261
6M3V 355 bp di-nucleosome harboring cohesive DNA termini Deposited 2020-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded K POTASSIUM ION × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
Resolution 4.60 Å R-free 0.261
6M44 355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant) Deposited 2020-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
Resolution 3.81 Å R-free 0.286
6O1D Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA Deposited 2019-02-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；blot for 2.5 sec before plunging
Resolution 3.40 Å
6R8Y Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6R8Z Cryo-EM structure of NCP_THF2(-1)-UV-DDB Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6R90 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6R91 Cryo-EM structure of NCP_THF2(-3)-UV-DDB Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6R92 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6R93 Cryo-EM structure of NCP-6-4PP Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6R94 Cryo-EM structure of NCP_THF2(-3) Deposited 2019-04-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6T79 Structure of a human nucleosome at 3.2 A resolution Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.20 Å
6T7A Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 3.70 Å
6T7B Structure of human Sox2 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 5.10 Å
6T7C Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.00 Å
6T7D Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
Resolution 4.40 Å
6T90 OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2019-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded PTD PENTANEDIAL × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
6T93 Nucleosome with OCT4-SOX2 motif at SHL-6 Deposited 2019-10-25 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.49 Å
6V92 RSC-NCP Deposited 2019-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 33 PDB declaration: 35-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
6YOV OCT4-SOX2-bound nucleosome - SHL+6 Deposited 2020-04-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
7BWD Structure of Dot1L-H2BK34ub Nucleosome Complex Deposited 2020-04-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.32 Å
7BXT The cryo-EM structure of CENP-A nucleosome in complex with CENP-C peptide and CENP-N N-terminal domain Deposited 2020-04-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7BY0 The cryo-EM structure of CENP-A nucleosome in complex with the phosphorylated CENP-C Deposited 2020-04-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7C0M Human cGAS-nucleosome complex Deposited 2020-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7CCQ Structure of the 1:1 cGAS-nucleosome complex Deposited 2020-06-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 16–118（103 aa）
Chain G 16–118（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7CCR Structure of the 2:2 cGAS-nucleosome complex Deposited 2020-06-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 16–118（103 aa）
Chain G 16–118（103 aa）
Chain N 16–118（103 aa）
Chain R 16–118（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
7COW 353 bp di-nucleosome harboring cohesive DNA termini with linker histone H1.0 Deposited 2020-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 3 K POTASSIUM ION × 5 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；potassium acetate, calcium chloride, potassium chloride
Resolution 2.86 Å R-free 0.297
7D1Z Cryo-EM structure of SET8-nucleosome complex Deposited 2020-09-15 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7D20 Cryo-EM structure of SET8-CENP-A-nucleosome complex Deposited 2020-09-15 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7DBP Linker histone defines structure and self-association behaviour of the 177 bp human chromosome Deposited 2020-10-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7K5X Cryo-EM structure of a chromatosome containing human linker histone H1.0 Deposited 2020-09-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
7K5Y Cryo-EM structure of a chromatosome containing human linker histone H1.4 Deposited 2020-09-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7K60 Cryo-EM structure of a chromatosome containing human linker histone H1.10 Deposited 2020-09-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
7K61 Cryo-EM structure of 197bp nucleosome aided by scFv Deposited 2020-09-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
7K63 Cryo-EM structure of a chromatosome containing chimeric linker histone gH1.10-ncH1.4 Deposited 2020-09-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
7LYA Cryo-EM structure of the human nucleosome core particle with linked histone proteins H2A and H2B Deposited 2021-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
7LYB Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Deposited 2021-03-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
7LYC Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Deposited 2021-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
7NL0 Cryo-EM structure of the Lin28B nucleosome core particle Deposited 2021-02-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7PET The 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 36-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Chain m 1–130（130 aa）
Chain q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.50 Å
7PEU Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7PEV Nucleosome stack of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7PEW Nucleosome 1 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7PEX Nucleosome 2 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PEY Nucleosome 3 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7PEZ Nucleosome 4 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain m 1–130（130 aa）
Chain q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
7PF0 Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7PF2 Nucleosome stack of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
7PF3 Nucleosome 4 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain m 1–130（130 aa）
Chain q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF4 Nucleosome 3 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PF5 Nucleosome 2 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7PF6 Nucleosome 1 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7PFA Trinucleosome of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.70 Å
7PFC Nucleosome stack of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
7PFD Nucleosome 1 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFE Nucleosome 2 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFF Nucleosome 3 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7PFT Trinucleosome of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.80 Å
7PFU Nucleosome stack of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
7PFV Nucleosome 1 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7PFW Nucleosome 2 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.20 Å
7PFX Nucleosome 3 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7V90 Telomeric mononucleosome Deposited 2021-08-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7V96 Telomeric Dinucleosome Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
7V99 catalytic core of human telomerase holoenzyme Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric
Chain K 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7V9C Telomeric Dinucleosome in open state Deposited 2021-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7V9J Telomeric trinucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.00 Å
7V9K Telomeric tetranucleosome Deposited 2021-08-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.10 Å
7V9S Telomeric trinucleosome in open state Deposited 2021-08-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 11.00 Å
7VA4 Telomeric tetranucleosome in open state Deposited 2021-08-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain U 1–130（130 aa）
Chain Y 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 14.00 Å
7VZ4 Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA sequence Deposited 2021-11-15 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 1.89 Å
7W9V Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) Deposited 2021-12-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XD1 cryo-EM structure of unmodified nucleosome Deposited 2022-03-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 11–119（109 aa）
Chain G 11–119（109 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain W 1–130（130 aa）
Chain a 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.51 Å R-free 0.280
7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Chain g 1–130（130 aa）
Chain k 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.51 Å R-free 0.280
7XVM Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 18 CL CHLORIDE ION × 3 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 2.84 Å R-free 0.259
7XX5 Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.19 Å R-free 0.259
7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CA CALCIUM ION × 21 K POTASSIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.39 Å R-free 0.296
7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric
Chain W 1–130（130 aa）
Chain a 1–130（130 aa）
Chain g 1–130（130 aa）
Chain k 1–130（130 aa）
Not recorded CA CALCIUM ION × 26 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 3.39 Å R-free 0.296
7XZX Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain Deposited 2022-06-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.53 Å
7XZY Cryo-EM structure of the nucleosome containing 193 base-pair DNA with a p53 target sequence Deposited 2022-06-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
7XZZ Cryo-EM structure of the nucleosome in complex with p53 Deposited 2022-06-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7Y00 Cryo-EM structure of the nucleosome containing 169 base-pair DNA with a p53 target sequence Deposited 2022-06-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
7Y7I chicken KNL2 in complex with the CENP-A nucleosome Deposited 2022-06-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：L51M, L58M, L93M Mutation：L51M, L58M, L93M No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
7ZI4 Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Deposited 2022-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain K 1–130（130 aa）
Chain O 1–130（130 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；4uL of sample applied to Quantifoil R2/2 Cu 300 mesh grids. blot parameters were wait time 30 sec, blot time 0.5 sec, blot force -8
Resolution 3.20 Å
8G57 Structure of nucleosome-bound Sirtuin 6 deacetylase Deposited 2023-02-11 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；12.5 mM HEPES pH 7.5, 60 mM KCl, 1.5% glycerol, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8GRM Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome Deposited 2022-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 12–120（109 aa）
Chain G 12–120（109 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8HAG Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (3.2 angstrom resolution) Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8HAH Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (3.9 angstrom resolution) Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8HAI Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (4.7 angstrom resolution) Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
8HAJ Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (4.8 angstrom resolution) Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
8HAK Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (4.5 angstrom resolution) Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
8HAL Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 1 Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8HAM Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 2 Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
8HAN Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 3 Deposited 2022-10-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8HQY Cryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom Deposited 2022-12-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 14–119（106 aa）
Chain G 14–119（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8HR1 Cryo-EM structure of SSX1 bound to the unmodified nucleosome at a resolution of 3.02 angstrom Deposited 2022-12-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 14–119（106 aa）
Chain G 14–119（106 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8I17 Structural basis for H2A-H2B recognitions by human Spt16 Deposited 2023-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 14–113（100 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES monohydrate pH 6.0, 14% w/v Polyethylene glycol 4,000
Resolution 1.98 Å R-free 0.211
8I17 Structural basis for H2A-H2B recognitions by human Spt16 Deposited 2023-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 14–113（100 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES monohydrate pH 6.0, 14% w/v Polyethylene glycol 4,000
Resolution 1.98 Å R-free 0.211
8I17 Structural basis for H2A-H2B recognitions by human Spt16 Deposited 2023-01-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 14–113（100 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES monohydrate pH 6.0, 14% w/v Polyethylene glycol 4,000
Resolution 1.98 Å R-free 0.211
8IEG Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deposited 2023-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 11–119（109 aa）
Chain G 11–119（109 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8IEJ RNF20-RNF40/hRad6A-Ub/nucleosome complex Deposited 2023-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 11–119（109 aa）
Chain G 11–119（109 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
8IHL Overlapping tri-nucleosome Deposited 2023-02-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain O 1–130（130 aa）
Chain S 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.64 Å
8JBX Human canonical 601 DNA nucleosome Deposited 2023-05-09 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
8JCC Human histone H2B variant H2BFWT Cryo-EM structure with 601 DNA sequence Deposited 2023-05-10 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
8JCD Human H2BFWTH100R nucleosome with 601 DNA Deposited 2023-05-11 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8JHG Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 16–130（115 aa）
Chain G 16–130（115 aa）
Not recorded ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.58 Å
8JL9 Cryo-EM structure of the human nucleosome with scFv Deposited 2023-06-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
8JLA Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 Deposited 2023-06-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 11–130（120 aa）
Chain G 11–130（120 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8JLB Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant Deposited 2023-06-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.36 Å
8JLD Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail Deposited 2023-06-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
8JND The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-06-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 19-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
8JNE The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding Deposited 2023-06-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.68 Å
8JNF The cryo-EM structure of the RAD51 filament bound to the nucleosome Deposited 2023-06-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.91 Å
8KB5 Cryo-EM structure of the human nucleosome containing H3.8 Deposited 2023-08-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.26 Å
8KCY Structure of nucleosome complexed with two DEK molecules Deposited 2023-08-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8KD1 Structure of nucleosome complexed with one DEK molecule Deposited 2023-08-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8KE0 Structure of H1.2 bound to the nucleosome Deposited 2023-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8OSJ Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Deposited 2023-04-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
8OSK Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) Deposited 2023-04-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8OSL Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement) Deposited 2023-04-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.90 Å
8OTS OCT4 and MYC-MAX co-bound to a nucleosome Deposited 2023-04-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8OTT MYC-MAX bound to a nucleosome at SHL+5.8 Deposited 2023-04-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 9–117（109 aa）
Not recorded PTD PENTANEDIAL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8Q36 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound) Deposited 2023-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain CCC 14–120（107 aa）
Chain GGG 14–120（107 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0].
Resolution 2.60 Å R-free 0.262
8Q3E High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain CCC 14–120（107 aa）
Chain GGG 14–120（107 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.17 Å R-free 0.270
8Q3M Structure of Nucleosome Core with a Bound Kaposi Sarcoma Associated Herpesvirus LANA Peptide Having a Methionine to Ornithine Substitution Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain CCC 14–120（107 aa）
Chain GGG 14–120（107 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.50 Å R-free 0.268
8Q3X Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound) Deposited 2023-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain CCC 14–120（107 aa）
Chain GGG 14–120（107 aa）
Not recorded AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
Resolution 2.30 Å R-free 0.262
8RGM Cryo-EM structure of nucleosome containing Widom603 DNA Deposited 2023-12-14 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8SMW Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SMX Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMY Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SMZ Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN0 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8SN1 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8SN2 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：R11S, K15C Mutation：R11S, K15C ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8TXV Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Deposited 2023-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：K13S Mutation：K13S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8TXW Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Deposited 2023-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：K13S Mutation：K13S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TXX Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Deposited 2023-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 12–130（119 aa）
Chain G 12–130（119 aa）
Mutation：K13S Mutation：K13S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8U13 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) Deposited 2023-08-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Mutation：K13S Mutation：K13S ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8U14 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Deposited 2023-08-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Mutation：K13S Mutation：K13S ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8U9S Cryo-EM structure of NRCAM nucleosome aided by scFv Deposited 2023-09-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8UBJ Cryo-EM structure of NRCAM nucleosome aided by scFv (3D Flex map) Deposited 2023-09-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8UBK Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome Deposited 2023-09-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8UBL Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome (3D Flex map) Deposited 2023-09-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8UPF Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Deposited 2023-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 13–130（118 aa）
Chain G 13–130（118 aa）
Mutation：R11S Mutation：R11S ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–106（94 aa）
Not recorded CL CHLORIDE ION × 7 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.34 Å R-free 0.236
8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain a 13–106（94 aa）
Not recorded CL CHLORIDE ION × 14 GOL GLYCEROL × 2 ZN ZINC ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.34 Å R-free 0.236
8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–106（94 aa）
Not recorded CL CHLORIDE ION × 17 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.30 Å R-free 0.206
8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain a 13–106（94 aa）
Not recorded CL CHLORIDE ION × 19 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.30 Å R-free 0.206
8UQA Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain K 13–106（94 aa）
Mutation：C85K in UbcH5c NA SODIUM ION × 3 ZN ZINC ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.0 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.05 Å R-free 0.231
8UQB Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 1) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–106（94 aa）
Mutation：C85K in UbcH5c ZN ZINC ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 50 mM BIS-TRIS propane, pH 7.0, 1 M NaCl
Resolution 2.48 Å R-free 0.260
8UQC Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 2) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–106（94 aa）
Mutation：C85K in UbcH5c ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
Resolution 2.61 Å R-free 0.252
8UQD Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (condition 2. RING not modeled in density) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 13–106（94 aa）
Mutation：C85K in UbcH5c No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
Resolution 3.89 Å R-free 0.322
8UQE Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 26-residue linker (RING not modeled in density) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 13–106（94 aa）
Mutation：S22R,C85K in UbcH5c No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (10 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M imidazole, pH 6.5, 1.0 M sodium acetate
Resolution 3.56 Å R-free 0.268
8VFX Cryo-EM structure of 186bp ALBN1 nucleosome aided by scFv Deposited 2023-12-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
8VFY Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1) Deposited 2023-12-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
8VFZ Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2) Deposited 2023-12-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8VG0 Cryo-EM structure of GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8VG1 Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
8VG2 Cryo-EM structure of FoxA1 and GATA4 in complex with H14 chromatosome Deposited 2023-12-22 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8VLR Cryo-EM structure of native H2AK119bu nucleosome at 2.6 Deposited 2024-01-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 12–119（108 aa）
Chain G 12–119（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Tris-HCl, pH 7.5, 50 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8W9D Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8W9E Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 7 K POTASSIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8W9F Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Deposited 2023-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 11–119（109 aa）
Chain G 11–119（109 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8X7I Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Deposited 2023-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 11–121（111 aa）
Chain G 11–119（109 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8X7J Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Deposited 2023-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 12–119（108 aa）
Chain G 11–118（108 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8X7K Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) Deposited 2023-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 15–119（105 aa）
Chain G 11–118（108 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8XBT The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.12 Å
8XBU The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.24 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8Y3C Cryo-EM structure of the overlapping di-nucleosome (closed form) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.21 Å
8Y3D Cryo-EM structure of the overlapping di-nucleosome (intermediate form2) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
8Y3E Cryo-EM structure of the overlapping di-nucleosome (open form) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.32 Å
8Y3F Cryo-EM structure of the overlapping di-nucleosome (intermediate form1) Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.54 Å
8YBJ Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence Deposited 2024-02-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.38 Å
8YBK Cryo-EM structure of the human nucleosome containing the H3.1 E97K mutant Deposited 2024-02-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.69 Å
8YNY Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome Deposited 2024-03-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: 13-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.52 Å
8YTI Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2024-03-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded CL CHLORIDE ION × 8 CA CALCIUM ION × 52 K POTASSIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45 mM CaCl2, 25 mM KCl, 10 mM Na-acetate (pH 4.5)
Resolution 2.70 Å R-free 0.267
8YV8 Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence. Deposited 2024-03-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8ZJR Structure of nucleosome-bound RFX5 complex Deposited 2024-05-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8ZJT Structure of free nucleosome Deposited 2024-05-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9BE5 Cryo-EM structure of Human Nucleosome collected by EPU on Glacios at 3.3 Angstrom resolution Deposited 2024-04-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain G 15–119（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9BE6 Cryo-EM structure of Human Nucleosome collected by Leginon on Krios at 3.0 Angstrom resolution Deposited 2024-04-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain G 15–119（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9GE5 CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric
Chain S 12–119（108 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
9GEL CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain S 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.86 Å
9GEV CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain O 2–130（129 aa）
Chain S 2–130（129 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9GF6 CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain O 2–130（129 aa）
Chain S 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9GFB CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain O 2–130（129 aa）
Chain S 2–130（129 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
9GFM CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain O 14–119（106 aa）
Chain S 9–119（111 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9GW2 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Deposited 2024-09-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.84 Å
9IGW Ku70/80 bound to 147 bp nucleosome Deposited 2025-02-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
9IGX Ku70/80 bound to 153 bp nucleosome Deposited 2025-02-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 12–121（110 aa）
Chain G 12–121（110 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å
9IPU cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Deposited 2024-07-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9J0N Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 27 PDB declaration: 30-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9J0O Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9J0P Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc) Deposited 2024-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9J8M Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (High mobility complex) Deposited 2024-08-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.82 Å
9J8N Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (Low mobility complex) Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 32-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.14 Å
9J8O Cryo-EM structure of BAF-Lamin A/C IgF-H1-nucleosome complex Deposited 2024-08-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 28-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
9J8W Cryo-EM structure of NCP-UV-DDB complex containing CPD Deposited 2024-08-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
9JC6 Human H2BW2 nucleosome Deposited 2024-08-28 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
9KQO cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome Deposited 2024-11-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9L1X hDEK-nucleosome complex (conformation 1) Deposited 2024-12-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–120（119 aa）
Chain G 2–120（119 aa）
Not recorded UNX UNKNOWN LIGAND × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
9L22 hDEK-nucleosome complex (conformation 2) Deposited 2024-12-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded UNX UNKNOWN LIGAND × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9R04 p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample) Deposited 2025-04-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9R2M p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, composite map) Deposited 2025-04-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9R2P p53 bound to nucleosome at position SHL+5.9 (crosslinked sample) Deposited 2025-04-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
9R2Q p53 bound to nucleosome at position SHL-5.7 (non-crosslinked sample) Deposited 2025-04-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9RL4 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2025-06-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded PTD PENTANEDIAL × 16 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9RMC Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1 Deposited 2025-06-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9RN1 Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2 Deposited 2025-06-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
9RN2 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 Deposited 2025-06-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
9RZC State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Deposited 2025-07-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
9RZE State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Deposited 2025-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.53 Å
9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.72 Å
9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
9U5U The 1:1 cryo-EM structure of BAP1/ASXL1-K351Ub in complex with H2AK119Ub nucleosome Deposited 2025-03-21 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9UZ7 Cryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking Deposited 2025-05-16 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 2–130（129 aa）
Chain F 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；10 mM HEPES, pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution not provided
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9XSF Cryo-EM structure of H4S47GlcNAc nucleosome at 3.39 angstrom Deposited 2025-11-20 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.39 Å
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å
9ZEN Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2 Deposited 2025-11-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain C 11–121（111 aa）
Chain G 11–121（111 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
9ZEO Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1 Deposited 2025-11-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 11–121（111 aa）
Chain G 11–121（111 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

343 other PDB entries and 350 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H2A1B_HUMAN
Isoform —
PDB entities 7
Chains and sequence ranges Author chain C； PDBConstruct 1–129； UniProt 2–130 Author chain G； PDBConstruct 1–129； UniProt 2–130

Histone H2B type 2-E

Homo sapiens

UniProt Q16778

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 15 DNA 2 PDB declaration: 17-meric（17） Consistent with all polymer counts Chain D； UniProt 2–126 Chain H； UniProt 2–126 Not recorded Ubiquitin × 1 （P0CG47） [histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D × 1 （A0A6P6IDI8,O14686） Retinoblastoma-binding protein 5 × 1 （Q15291） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 2 （P04908） DNA (145-MER) × 1 WD repeat-containing protein 5 × 1 （P61964） DNA (145-MER) × 1 Protein dpy-30 homolog × 2 （Q9C005） ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.63 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9YLE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4NFT Crystal structure of human lnkH2B-h2A.Z-Anp32e Deposited 2013-11-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 34–126（93 aa） Fragment：UNP residues 34-126, 16-114
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；0.2M Sodium thiocyanate, 20%(w/v) polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.61 Å R-free 0.273
4NFT Crystal structure of human lnkH2B-h2A.Z-Anp32e Deposited 2013-11-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 34–126（93 aa） Fragment：UNP residues 34-126, 16-114
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；0.2M Sodium thiocyanate, 20%(w/v) polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.61 Å R-free 0.273
4NFT Crystal structure of human lnkH2B-h2A.Z-Anp32e Deposited 2013-11-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 34–126（93 aa） Fragment：UNP residues 34-126, 16-114
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；0.2M Sodium thiocyanate, 20%(w/v) polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.61 Å R-free 0.273
4NFT Crystal structure of human lnkH2B-h2A.Z-Anp32e Deposited 2013-11-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 34–126（93 aa） Fragment：UNP residues 34-126, 16-114
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；0.2M Sodium thiocyanate, 20%(w/v) polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.61 Å R-free 0.273
6A7U Crystal structure of histone H2A.Bbd-H2B dimer Deposited 2018-07-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–126（126 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.1M sodium citrate tribasic dihydrate pH5.5 38% PEG 200
Resolution 2.60 Å R-free 0.263
6KBB Role of the DEF/Y motif of Swc5 in histone H2A.Z deposition Deposited 2019-06-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 27–126（100 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.1M sodium acetate tribasic dihydrate, pH 5.3, 19.5% PEG 1000
Resolution 2.37 Å R-free 0.226
6KBB Role of the DEF/Y motif of Swc5 in histone H2A.Z deposition Deposited 2019-06-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 27–126（100 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.1M sodium acetate tribasic dihydrate, pH 5.3, 19.5% PEG 1000
Resolution 2.37 Å R-free 0.226
6M4D Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6M4G Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6M4H Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7BXT The cryo-EM structure of CENP-A nucleosome in complex with CENP-C peptide and CENP-N N-terminal domain Deposited 2020-04-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7EA8 Human SETD2 bound to a nucleosome containing oncohistone mutations Deposited 2021-03-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7U0G structure of LIN28b nucleosome bound 3 OCT4 Deposited 2022-02-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
7U0I Structure of LIN28b nucleosome bound 2 OCT4 Deposited 2022-02-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
7U0J Structure of 162bp LIN28b nucleosome Deposited 2022-02-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8DK5 Structure of 187bp LIN28b nucleosome with site 0 mutation Deposited 2022-07-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
8EVG 162bp CX3CR1 nucleosome (further classified with better nucleosome end) Deposited 2022-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
8EVH CX3CR1 nucleosome and wild type PU.1 complex Deposited 2022-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
8EVI CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations Deposited 2022-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.64 Å
8EVJ CX3CR1 nucleosome bound PU.1 and C/EBPa Deposited 2022-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8H1T Cryo-EM structure of BAP1-ASXL1 bound to chromatosome Deposited 2022-10-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8SPS High resolution structure of ESRRB nucleosome bound OCT4 at site a and site b Deposited 2023-05-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8SPU Structure of ESRRB nucleosome bound OCT4 at site c Deposited 2023-05-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8SYP Genomic CX3CR1 nucleosome Deposited 2023-05-25 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 34–124（91 aa）
Not recorded CL CHLORIDE ION × 7 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.34 Å R-free 0.236
8UQ8 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain a 34–124（91 aa）
Not recorded CL CHLORIDE ION × 14 GOL GLYCEROL × 2 ZN ZINC ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (9.5 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.34 Å R-free 0.236
8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 34–124（91 aa）
Not recorded CL CHLORIDE ION × 17 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.30 Å R-free 0.206
8UQ9 Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain a 34–124（91 aa）
Not recorded CL CHLORIDE ION × 19 GOL GLYCEROL × 3 ZN ZINC ION × 2 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.8 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.30 Å R-free 0.206
8UQA Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain K 34–124（91 aa）
Mutation：C85K in UbcH5c NA SODIUM ION × 3 ZN ZINC ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (8.0 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Resolution 2.05 Å R-free 0.231
8UQB Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 1) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 34–124（91 aa）
Mutation：C85K in UbcH5c ZN ZINC ION × 2 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 50 mM BIS-TRIS propane, pH 7.0, 1 M NaCl
Resolution 2.48 Å R-free 0.260
8UQC Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (crystallization condition 2) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 34–124（91 aa）
Mutation：C85K in UbcH5c ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
Resolution 2.61 Å R-free 0.252
8UQD Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker (condition 2. RING not modeled in density) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 34–124（91 aa）
Mutation：C85K in UbcH5c No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (12 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 4% tacsimate, pH 6, 13.5% PEG3350
Resolution 3.89 Å R-free 0.322
8UQE Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 26-residue linker (RING not modeled in density) Deposited 2023-10-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 34–124（91 aa）
Mutation：S22R,C85K in UbcH5c No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；Crystals were obtained by mixing 2 microliters of the protein fusion (10 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M imidazole, pH 6.5, 1.0 M sodium acetate
Resolution 3.56 Å R-free 0.268
8YJF Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and an H2A-H2B dimer Deposited 2024-03-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–126（126 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M calcium acetate, 0.1 M Sodium cacodylate pH 5.5, 12% (w/v) PEG 8000
Resolution 4.40 Å R-free 0.312
9GCG CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Deposited 2024-08-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain P 2–126（125 aa）
Chain T 2–126（125 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å
9GE4 CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Deposited 2024-08-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain P 2–126（125 aa）
Chain T 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
9GEL CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain T 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.86 Å
9GEV CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain P 2–126（125 aa）
Chain T 2–126（125 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9GF6 CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain P 2–126（125 aa）
Chain T 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9GFB CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain P 2–126（125 aa）
Chain T 2–126（125 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
9GFM CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain P 31–126（96 aa）
Chain T 32–124（93 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å

39 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H2B2E_HUMAN
Isoform —
PDB entities 8
Chains and sequence ranges Author chain D； PDBConstruct 1–125； UniProt 2–126 Author chain H； PDBConstruct 1–125； UniProt 2–126

WD repeat-containing protein 5

Homo sapiens

UniProt P61964

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 15 DNA 2 PDB declaration: 17-meric（17） Consistent with all polymer counts Chain R； UniProt 1–334 Not recorded Ubiquitin × 1 （P0CG47） [histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D × 1 （A0A6P6IDI8,O14686） Retinoblastoma-binding protein 5 × 1 （Q15291） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 2-E × 2 （Q16778） DNA (145-MER) × 1 DNA (145-MER) × 1 Protein dpy-30 homolog × 2 （Q9C005） ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.63 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9YLE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10TC Structure of WDR5 bound to RbBP5 (D376N) Deposited 2026-02-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 31–334（304 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.15 M Ammonium citrate, 18% PEG3350
Resolution 2.20 Å R-free 0.243
10TC Structure of WDR5 bound to RbBP5 (D376N) Deposited 2026-02-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 31–334（304 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.15 M Ammonium citrate, 18% PEG3350
Resolution 2.20 Å R-free 0.243
10TC Structure of WDR5 bound to RbBP5 (D376N) Deposited 2026-02-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 31–334（304 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.15 M Ammonium citrate, 18% PEG3350
Resolution 2.20 Å R-free 0.243
10TC Structure of WDR5 bound to RbBP5 (D376N) Deposited 2026-02-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 31–334（304 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.15 M Ammonium citrate, 18% PEG3350
Resolution 2.20 Å R-free 0.243
24XN Structure of WDR5 F263A variant in complex with MBD3C Deposited 2026-03-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.15 ammonium sulfate, 0.1 M sodium HEPES, pH7.0, 20% w/v PEG 4000
Resolution 1.57 Å R-free 0.212
24XN Structure of WDR5 F263A variant in complex with MBD3C Deposited 2026-03-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.15 ammonium sulfate, 0.1 M sodium HEPES, pH7.0, 20% w/v PEG 4000
Resolution 1.57 Å R-free 0.212
24XP Crystal structure of WDR5 F133A variant in complex with MBD3C Deposited 2026-03-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M sodium acetate (pH 5.0), 20% (w/v) PEG 4000
Resolution 1.30 Å R-free 0.180
24XP Crystal structure of WDR5 F133A variant in complex with MBD3C Deposited 2026-03-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M sodium acetate (pH 5.0), 20% (w/v) PEG 4000
Resolution 1.30 Å R-free 0.180
2CNX WDR5 and Histone H3 Lysine 4 dimethyl complex at 2.1 angstrom Deposited 2006-05-25 Different construct Different oligomeric state Different experimental method Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 20–334（315 aa） Fragment：RESIDUES 20-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.223
2CO0 WDR5 and unmodified Histone H3 complex at 2.25 Angstrom Deposited 2006-05-25 Different construct Different oligomeric state Different experimental method Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 20–334（315 aa） Fragment：RESIDUES 20-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.25 Å R-free 0.226
2CO0 WDR5 and unmodified Histone H3 complex at 2.25 Angstrom Deposited 2006-05-25 Different construct Different oligomeric state Different experimental method Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 20–334（315 aa） Fragment：RESIDUES 20-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.25 Å R-free 0.226
2G99 Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5 Deposited 2006-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 27–334（308 aa） Fragment：residues 27-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG 4000, 10% isopropanol, 0.1M HEPES, pH7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.90 Å R-free 0.243
2G99 Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5 Deposited 2006-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 27–334（308 aa） Fragment：residues 27-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG 4000, 10% isopropanol, 0.1M HEPES, pH7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.90 Å R-free 0.243
2G9A Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5 Deposited 2006-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 29–334（306 aa） Fragment：;'residues 24-334 ;
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG, 0.2M ammonium acetate, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.70 Å R-free 0.286
2GNQ Structure of wdr5 Deposited 2006-04-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–334（334 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；20%peg5k mme, bis-tris 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Resolution 1.80 Å R-free 0.192
2H13 Crystal structure of WDR5/histone H3 complex Deposited 2006-05-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa） Fragment：Residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；20-30% PEG3350, 0.1 M HEPES, pH 7.5, 0.05 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP
Resolution 1.58 Å R-free 0.200
2H14 Crystal of WDR5 (apo-form) Deposited 2006-05-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa） Fragment：Residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；20-30% PEG 3350 0.1M Hepes 0.05M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP
Resolution 1.48 Å R-free 0.197
2H68 Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-05-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.79 Å R-free 0.192
2H68 Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-05-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.79 Å R-free 0.192
2H6K Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-05-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris, HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.89 Å R-free 0.190
2H6K Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-05-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris, HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.89 Å R-free 0.190
2H6N Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-05-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.50 Å R-free 0.198
2H6N Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-05-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.50 Å R-free 0.198
2H6Q Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-06-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.87 Å R-free 0.185
2H6Q Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-06-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.87 Å R-free 0.185
2H9L WDR5delta23 Deposited 2006-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；20% PEG 5000 MME, 0.1M Bis-Tris 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Resolution 1.75 Å R-free 0.201
2H9M WDR5 in complex with unmodified H3K4 peptide Deposited 2006-06-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；20% PEG 3350, 0.2M di-Na Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.90 Å R-free 0.257
2H9M WDR5 in complex with unmodified H3K4 peptide Deposited 2006-06-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；20% PEG 3350, 0.2M di-Na Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.90 Å R-free 0.257
2H9N WDR5 in complex with monomethylated H3K4 peptide Deposited 2006-06-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.00 Å R-free 0.279
2H9N WDR5 in complex with monomethylated H3K4 peptide Deposited 2006-06-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.00 Å R-free 0.279
2H9P WDR5 in complex with trimethylated H3K4 peptide Deposited 2006-06-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；300 K；30% PEG4000, 0.2M Ammonium Acetate and 0.1M Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.91 Å R-free 0.203
2O9K WDR5 in Complex with Dimethylated H3K4 Peptide Deposited 2006-12-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；20% PEG 5000 MME, 0.1M BIS-TRIS, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K, pH 6.50
Resolution 1.90 Å R-free 0.226
2O9K WDR5 in Complex with Dimethylated H3K4 Peptide Deposited 2006-12-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；20% PEG 5000 MME, 0.1M BIS-TRIS, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K, pH 6.50
Resolution 1.90 Å R-free 0.226
3EG6 Structure of WDR5 bound to MLL1 peptide Deposited 2008-09-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：WD-repeat domain (UNP residues 23-334)
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；298 K；30% PEG 3350, 30 mM (NH4)2SO4, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.72 Å R-free 0.240
3EMH Structural basis of WDR5-MLL interaction Deposited 2008-09-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 25–334（310 aa） Fragment：UNP residues 25-334
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 15-20% PEG 3350, 60mM Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.37 Å R-free 0.200
3MXX Crystal structure of WDR5 mutant (S62A) Deposited 2010-05-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa） Fragment：RESIDUES 31-334
Mutation：S62A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；18% PEG 3350, 0.1M Hepes, 18mM (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.05 Å R-free 0.239
3N0D Crystal structure of WDR5 mutant (W330F) Deposited 2010-05-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa） Fragment：RESIDUES 31-334
Mutation：W330F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；18% PEG 3350, 0.1M Hepes, 14mM (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.233
3N0E Crystal structure of WDR5 mutant (W330Y) Deposited 2010-05-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa） Fragment：RESIDUES 31-334
Mutation：W330Y No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；18% PEG 3350, 0.1M Hepes, 14mM (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.323
3P4F Structural and biochemical insights into MLL1 core complex assembly and regulation. Deposited 2010-10-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 22–334（313 aa） Fragment：unp residues 1-308
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；0.2 M ammonium citrate (buffered with hydrochloric acid/sodium hydroxide to pH 7.0) and 18% PEG3350, VAPOR DIFFUSION, HANGING DROP
Resolution 2.35 Å R-free 0.249
3PSL Fine-tuning the stimulation of MLL1 methyltransferase activity by a histone H3 based peptide mimetic Deposited 2010-12-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa） Fragment：WDR5 (unp residues 21-334)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；50 mM NaAcetate, 100 mM NH4 SO4 , and 20% PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.205
3PSL Fine-tuning the stimulation of MLL1 methyltransferase activity by a histone H3 based peptide mimetic Deposited 2010-12-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 21–334（314 aa） Fragment：WDR5 (unp residues 21-334)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；50 mM NaAcetate, 100 mM NH4 SO4 , and 20% PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.205
3SMR Crystal structure of human WD repeat domain 5 with compound Deposited 2011-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded NP7 2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 8 UNX UNKNOWN LIGAND × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；24% PEG3350,9.2M NH4 Acetate, 0.1 Bis Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 1.82 Å R-free 0.206
3SMR Crystal structure of human WD repeat domain 5 with compound Deposited 2011-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa）
Not recorded NP7 2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 6 UNX UNKNOWN LIGAND × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；24% PEG3350,9.2M NH4 Acetate, 0.1 Bis Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 1.82 Å R-free 0.206
3SMR Crystal structure of human WD repeat domain 5 with compound Deposited 2011-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 24–334（311 aa）
Not recorded NP7 2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 5 UNX UNKNOWN LIGAND × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；24% PEG3350,9.2M NH4 Acetate, 0.1 Bis Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 1.82 Å R-free 0.206
3SMR Crystal structure of human WD repeat domain 5 with compound Deposited 2011-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 24–334（311 aa）
Not recorded NP7 2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 4 UNX UNKNOWN LIGAND × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；24% PEG3350,9.2M NH4 Acetate, 0.1 Bis Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 1.82 Å R-free 0.206
3UR4 Crystal structure of human WD repeat domain 5 with compound Deposited 2011-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded 0BW methyl 3-[(3-methoxybenzoyl)amino]-4-(4-methylpiperazin-1-yl)benzoate × 1 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 4 SO4 SULFATE ION × 2 UNX UNKNOWN LIGAND × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；297 K；22% PEG 3350,0.1M A.S. ,0.1M Bis Tris pH 6.0 , VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 1.80 Å R-free 0.213
3UR4 Crystal structure of human WD repeat domain 5 with compound Deposited 2011-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa）
Not recorded 0BW methyl 3-[(3-methoxybenzoyl)amino]-4-(4-methylpiperazin-1-yl)benzoate × 1 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 2 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；297 K；22% PEG 3350,0.1M A.S. ,0.1M Bis Tris pH 6.0 , VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 1.80 Å R-free 0.213
3UVK Crystal structure of WDR5 in complex with the WDR5-interacting motif of MLL2 Deposited 2011-11-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa） Fragment：UNP residues 21-334
Not recorded BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；323 K；0.1 M ammonium sulfate, 24% PEG3350, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 323K
Resolution 1.40 Å R-free 0.192
3UVL Crystal structure of WDR5 in complex with the WDR5-interacting motif of MLL3 Deposited 2011-11-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa） Fragment：UNP residues 21-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；323 K；0.1 M ammonium acetate, 25% PEG3350, 0.1 M Bis-Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 323K
Resolution 2.20 Å R-free 0.220
3UVM Crystal structure of WDR5 in complex with the WDR5-interacting motif of MLL4 Deposited 2011-11-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa） Fragment：UNP residues 21-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.1 M ammonium sulfate, 25% PEG3350, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.57 Å R-free 0.198
3UVN Crystal structure of WDR5 in complex with the WDR5-interacting motif of SET1A Deposited 2011-11-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa） Fragment：UNP residues 21-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；25% PEG3350, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.79 Å R-free 0.230
3UVN Crystal structure of WDR5 in complex with the WDR5-interacting motif of SET1A Deposited 2011-11-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 21–334（314 aa） Fragment：UNP residues 21-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；25% PEG3350, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.79 Å R-free 0.230
3UVO Crystal structure of WDR5 in complex with the WDR5-interacting motif of SET1B Deposited 2011-11-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa） Fragment：UNP residues 21-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.1 M ammonium sulfate, 25% PEG3350, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.219
4A7J Symmetric Dimethylation of H3 Arginine 2 is a Novel Histone Mark that Supports Euchromatin Maintenance Deposited 2011-11-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa） Fragment：RESIDUES 21-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M HEPES PH 7.5; 60 MM AMMONIUM SULPHATE; 30% PEG 3350
Resolution 1.90 Å R-free 0.222
4CY1 Crystal structure of the KANSL1-WDR5 complex. Deposited 2014-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：RESIDUES 23-334
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；26% (W/V) PEG 3350, 0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS, PH 6.5.
Resolution 1.50 Å R-free 0.183
4CY1 Crystal structure of the KANSL1-WDR5 complex. Deposited 2014-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa） Fragment：RESIDUES 23-334
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；26% (W/V) PEG 3350, 0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS, PH 6.5.
Resolution 1.50 Å R-free 0.183
4CY2 Crystal structure of the KANSL1-WDR5-KANSL2 complex. Deposited 2014-04-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 23–334（312 aa） Fragment：RESIDUES 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.9；20% (W/V) PEG 3350, 0.2 M POTASSIUM NITRATE, PH 6.9.
Resolution 2.00 Å R-free 0.222
4ERQ X-ray structure of WDR5-MLL2 Win motif peptide binary complex Deposited 2012-04-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.3；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.3, hanging drop, temperature 294K
Resolution 1.91 Å R-free 0.200
4ERQ X-ray structure of WDR5-MLL2 Win motif peptide binary complex Deposited 2012-04-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.3；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.3, hanging drop, temperature 294K
Resolution 1.91 Å R-free 0.200
4ERQ X-ray structure of WDR5-MLL2 Win motif peptide binary complex Deposited 2012-04-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.3；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.3, hanging drop, temperature 294K
Resolution 1.91 Å R-free 0.200
4ERY X-ray structure of WDR5-MLL3 Win motif peptide binary complex Deposited 2012-04-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.5；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.5, hanging drop, temperature 294K
Resolution 1.30 Å R-free 0.209
4ERZ X-ray structure of WDR5-MLL4 Win motif peptide binary complex Deposited 2012-04-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.6；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.6, hanging drop, temperature 294K
Resolution 1.75 Å R-free 0.216
4ERZ X-ray structure of WDR5-MLL4 Win motif peptide binary complex Deposited 2012-04-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.6；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.6, hanging drop, temperature 294K
Resolution 1.75 Å R-free 0.216
4ERZ X-ray structure of WDR5-MLL4 Win motif peptide binary complex Deposited 2012-04-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.6；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.6, hanging drop, temperature 294K
Resolution 1.75 Å R-free 0.216
4ES0 X-ray structure of WDR5-SETd1b Win motif peptide binary complex Deposited 2012-04-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.6；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.6, hanging drop, temperature 294K
Resolution 1.82 Å R-free 0.242
4ESG X-ray structure of WDR5-MLL1 Win motif peptide binary complex Deposited 2012-04-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.2；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.2, hanging drop, temperature 294K
Resolution 1.70 Å R-free 0.193
4ESG X-ray structure of WDR5-MLL1 Win motif peptide binary complex Deposited 2012-04-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.2；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.2, hanging drop, temperature 294K
Resolution 1.70 Å R-free 0.193
4EWR X-ray structure of WDR5-SETd1a Win motif peptide binary complex Deposited 2012-04-27 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.6；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.6, hanging drop, temperature 294K
Resolution 1.50 Å R-free 0.198
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM8 Crystal structure of human WD repeat domain 5 with compound MM-102 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；30% PEG8000, 0.2 M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.249
4GM8 Crystal structure of human WD repeat domain 5 with compound MM-102 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；30% PEG8000, 0.2 M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.249
4GM8 Crystal structure of human WD repeat domain 5 with compound MM-102 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；30% PEG8000, 0.2 M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.249
4GM8 Crystal structure of human WD repeat domain 5 with compound MM-102 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；30% PEG8000, 0.2 M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.249
4GM9 Crystal structure of human WD repeat domain 5 with compound MM-401 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；30% PEG4000, 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Resolution 2.10 Å R-free 0.208
4GM9 Crystal structure of human WD repeat domain 5 with compound MM-401 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；30% PEG4000, 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Resolution 2.10 Å R-free 0.208
4GMB Crystal structure of human WD repeat domain 5 with compound MM-402 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% tert-butanol, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.78 Å R-free 0.247
4IA9 Crystal structure of human WD REPEAT DOMAIN 5 in complex with 2-chloro-4-fluoro-3-methyl-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide Deposited 2012-12-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded IA9 2-chloro-4-fluoro-3-methyl-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 2 UNX UNKNOWN LIGAND × 24 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；291 K；25% PEH 3500, 0.1 M Ammonium sulfate, 0.1 M BisTris pH5.5, vapor diffusion hanging drop, temperature 291K
Resolution 1.66 Å R-free 0.210
4O45 WDR5 in complex with influenza NS1 C-terminal tail Deposited 2013-12-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa） Fragment：UNP residues 24-334
Not recorded UNX UNKNOWN LIGAND × 17 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；25% PEG3350, 0.1 M ammonium sulfate, 0.1 M bis-tris, pH 6.5, temperature 291K
Resolution 1.87 Å R-free 0.212
4QL1 Crystal structure of human WDR5 in complex with compound OICR-9429 Deposited 2014-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded 35Q N-(4-(4-methylpiperazin-1-yl)-3'-(morpholinomethyl)-[1,1'-biphenyl]-3-yl)-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 UNX UNKNOWN LIGAND × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；25% PEG 3350, 0.2 M NH4oAC, 0.1 M BisTris pH6.5, vapor diffusion hanging drop, temperature 291K
Resolution 1.50 Å R-free 0.227
4QL1 Crystal structure of human WDR5 in complex with compound OICR-9429 Deposited 2014-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa）
Not recorded 35Q N-(4-(4-methylpiperazin-1-yl)-3'-(morpholinomethyl)-[1,1'-biphenyl]-3-yl)-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 UNX UNKNOWN LIGAND × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；25% PEG 3350, 0.2 M NH4oAC, 0.1 M BisTris pH6.5, vapor diffusion hanging drop, temperature 291K
Resolution 1.50 Å R-free 0.227
4QQE Crystal structure of WDR5, WD repeat domain 5 in complex with compound SGC-DS-MT-0345 Deposited 2014-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa） Fragment：UNP residues 24-334
Not recorded 37F N-[2-(4-methylpiperazin-1-yl)-5-(quinolin-3-yl)phenyl]-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 3 UNX UNKNOWN LIGAND × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；22% PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.80 Å R-free 0.218
4Y7R Crystal structure of WDR5 in complex with MYC MbIIIb peptide Deposited 2015-02-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1 M Tris 7.0, 25% PEG 8K
Resolution 1.90 Å R-free 0.188
5EAL Crystal structure of human WDR5 in complex with compound 9h Deposited 2015-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded 5ML 3-methyl-~{N}-[2-(4-methylpiperazin-1-yl)-5-quinolin-3-yl-phenyl]benzamide × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 8 UNX UNKNOWN LIGAND × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 5K MME, 0.1 M BisTris pH6.5
Resolution 1.80 Å R-free 0.211
5EAL Crystal structure of human WDR5 in complex with compound 9h Deposited 2015-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded 5ML 3-methyl-~{N}-[2-(4-methylpiperazin-1-yl)-5-quinolin-3-yl-phenyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 9 UNX UNKNOWN LIGAND × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 5K MME, 0.1 M BisTris pH6.5
Resolution 1.80 Å R-free 0.211
5EAM Crystal structure of human WDR5 in complex with compound 9o Deposited 2015-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded 5MN ~{N}-[5-(1~{H}-indol-5-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methyl-benzamide × 1 EDO 1,2-ETHANEDIOL × 1 UNX UNKNOWN LIGAND × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；25% PEG3350, 0.1M NH4SO4, 0.1 M BisTris pH6.5
Resolution 1.80 Å R-free 0.228
5EAM Crystal structure of human WDR5 in complex with compound 9o Deposited 2015-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded 5MN ~{N}-[5-(1~{H}-indol-5-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methyl-benzamide × 1 EDO 1,2-ETHANEDIOL × 4 UNX UNKNOWN LIGAND × 14 SO4 SULFATE ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；25% PEG3350, 0.1M NH4SO4, 0.1 M BisTris pH6.5
Resolution 1.80 Å R-free 0.228
5EAP Crystal structure of human WDR5 in complex with compound 9e Deposited 2015-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded 5MO N-[5-(2,3-dihydro-1-benzofuran-5-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methylbenzamide × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 5 UNX UNKNOWN LIGAND × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；28% PEG 2K MME, 0.1 M BisTris pH6.5
Resolution 1.73 Å R-free 0.241
5EAR Crystal structure of human WDR5 in complex with compound 9d Deposited 2015-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded 5MQ N-[5-(2,3-dihydro-1-benzofuran-7-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methylbenzamide × 1 EDO 1,2-ETHANEDIOL × 9 UNX UNKNOWN LIGAND × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；22% PEG 3350, 0.1M NH4SO4, 0.1 M BisTris pH5.5
Resolution 1.80 Å R-free 0.185
5EAR Crystal structure of human WDR5 in complex with compound 9d Deposited 2015-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded 5MQ N-[5-(2,3-dihydro-1-benzofuran-7-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methylbenzamide × 1 EDO 1,2-ETHANEDIOL × 10 UNX UNKNOWN LIGAND × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；22% PEG 3350, 0.1M NH4SO4, 0.1 M BisTris pH5.5
Resolution 1.80 Å R-free 0.185
5M23 Modulation of MLL1 Methyltransferase Activity Deposited 2016-10-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded 7DC 4-[(~{E})-[4-[[[(2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]amino]propanoyl]amino]-5-carbamimidamido-pentanoyl]amino]propanoyl]amino]methyl]phenyl]diazenyl]-~{N}-[(2~{S})-3-methyl-1-oxidanylidene-butan-2-yl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.02 M carboxylic acid 0.1 M bicine/Trizma base pH 8.5
Resolution 1.97 Å R-free 0.214
5M25 Modulation of MLL1 Methyltransferase Activity Deposited 2016-10-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded 7DU (2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]amino]propanoyl]amino]-5-carbamimidamido-~{N}-[(2~{S})-1-[[4-[(~{E})-[4-(hydroxymethyl)phenyl]diazenyl]phenyl]methylamino]-1-oxidanylidene-propan-2-yl]pentanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.02 M carboxylic acid 0.1 M bicine/Trizma base pH 8.5
Resolution 2.43 Å R-free 0.248
5SXM WDR5 in complex with MLL Win motif peptidomimetic Deposited 2016-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1M sodium citrate pH 5.6, 15% 2-propanol, and 17% PEG 4000, and 10mM ATP
Resolution 2.00 Å R-free 0.243
5SXM WDR5 in complex with MLL Win motif peptidomimetic Deposited 2016-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1M sodium citrate pH 5.6, 15% 2-propanol, and 17% PEG 4000, and 10mM ATP
Resolution 2.00 Å R-free 0.243
5VFC WDR5 bound to inhibitor MM-589 Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded 9BA N-{(3R,6S,9S,12R)-6-ethyl-12-methyl-9-[3-(N'-methylcarbamimidamido)propyl]-2,5,8,11-tetraoxo-3-phenyl-1,4,7,10-tetraazacyclotetradecan-12-yl}-2-methylpropanamide × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Na Bis-Tris pH 6.5, 26% PEG 8000 and 0.1 M ammonium sulfate
Resolution 1.64 Å R-free 0.174
6BYN Crystal structure of WDR5-Mb(S4) monobody complex Deposited 2017-12-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain W 31–334（304 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；28% PEG3350, 0.1 M BisTris pH 5.5
Resolution 2.69 Å R-free 0.248
6D9X Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded NA SODIUM ION × 1 FZM 2-phenyl-6,7-dihydro-5H-pyrrolo[1,2-a]imidazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.83 Å R-free 0.241
6DAI Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded DMS DIMETHYL SULFOXIDE × 2 G2V 6-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)-1-methylindoline × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.63 Å R-free 0.186
6DAK Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded G1Y N-{[3-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)phenyl]methyl}benzamide × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.60 Å R-free 0.188
6DAR Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded G2J N-(cyclopropylmethyl)-N-{[3-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)phenyl]methyl}-3-methoxybenzamide × 1 SO4 SULFATE ION × 2 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.88 Å R-free 0.195
6DAS Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded G2D N-[(1R)-6-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)-2,3-dihydro-1H-inden-1-yl]-3-methoxy-4-methylbenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.80 Å R-free 0.222
6DAS Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded G2D N-[(1R)-6-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)-2,3-dihydro-1H-inden-1-yl]-3-methoxy-4-methylbenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.80 Å R-free 0.222
6DY7 WDR5 in complex with a WIN site inhibitor Deposited 2018-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded HH7 N-[3-(2,4-dichlorophenoxy)propyl]-1H-imidazol-2-amine × 1 DMS DIMETHYL SULFOXIDE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.90 Å R-free 0.199
6DYA WDR5 in complex with a WIN site inhibitor Deposited 2018-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 30–334（305 aa）
Not recorded HHM N-[(3,5-dichlorophenyl)methyl]-3-[(1H-imidazol-1-yl)methyl]benzamide × 1 SO4 SULFATE ION × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 2.56 Å R-free 0.230
6E1Y Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-07-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded HLM N-[(1S)-1-(3-chlorophenyl)ethyl]-3-{[(4,5-dihydro-1H-imidazol-2-yl)amino]methyl}benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Bis-Tris pH 6.0 or Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.22 Å R-free 0.182
6E1Y Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-07-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded HLM N-[(1S)-1-(3-chlorophenyl)ethyl]-3-{[(4,5-dihydro-1H-imidazol-2-yl)amino]methyl}benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Bis-Tris pH 6.0 or Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.22 Å R-free 0.182
6E1Z Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity Deposited 2018-07-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded HLP 5-[(1H-imidazol-1-yl)methyl]furan-2-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.10 Å R-free 0.163
6E1Z Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity Deposited 2018-07-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded HLP 5-[(1H-imidazol-1-yl)methyl]furan-2-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.10 Å R-free 0.163
6E22 Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity Deposited 2018-07-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded HLS 3-{[(4,5-dihydro-1H-imidazol-2-yl)amino]methyl}-N-[(3,5-dimethoxyphenyl)methyl]-4-fluorobenzamide × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris pH 6.0 or Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.60 Å R-free 0.180
6E22 Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity Deposited 2018-07-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded HLS 3-{[(4,5-dihydro-1H-imidazol-2-yl)amino]methyl}-N-[(3,5-dimethoxyphenyl)methyl]-4-fluorobenzamide × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris pH 6.0 or Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.60 Å R-free 0.180
6E23 Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity Deposited 2018-07-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded HLJ N-[(3,4-dichlorophenyl)methyl]-3-(6-fluoro-2-methylpyridin-3-yl)-5-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris pH 6.0 or Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.66 Å R-free 0.209
6E23 Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity Deposited 2018-07-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded HLJ N-[(3,4-dichlorophenyl)methyl]-3-(6-fluoro-2-methylpyridin-3-yl)-5-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}benzamide × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris pH 6.0 or Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.66 Å R-free 0.209
6IAM Modulating Protein-Protein Interactions with Visible Light Peptide Backbone Switches Deposited 2018-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 29–334（306 aa）
Not recorded K POTASSIUM ION × 3 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate
Resolution 1.51 Å R-free 0.170
6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain R 1–334（334 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain R 1–334（334 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIW Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain R 1–334（334 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIX Cryo-EM structure of human MLL1-NCP complex, binding mode1 Deposited 2019-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain R 1–334（334 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6KIZ Cryo-EM structure of human MLL1-NCP complex, binding mode2 Deposited 2019-07-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain R 1–334（334 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6OFZ Crystal structure of human WDR5 Deposited 2019-04-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；295 K；100 mM Bis-Tris pH5.9, 32% PEG3350, 54.6 mM Ammonium Sulfate
Resolution 1.85 Å R-free 0.250
6OI0 Crystal structure of human WDR5 in complex with L-arginine Deposited 2019-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded ARG ARGININE × 1 SO4 SULFATE ION × 2 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；295 K；100 mM Bis-Tris pH 5.9; 32% PEG3350, 54.6 mM Ammonium Sulfate, 0.66 mM L-arginine
Resolution 1.92 Å R-free 0.201
6OI1 Crystal structure of human WDR5 in complex with monomethyl L-arginine Deposited 2019-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded SO4 SULFATE ION × 1 GOL GLYCEROL × 2 NMM (2S)-2-amino-5-[(N-methylcarbamimidoyl)amino]pentanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；295 K；100mM Bis-Tris pH 5.9, 32% PEG3350, 54.6 mM Ammonium Sulfate, 0.66 mM monomethyl L-arginine
Resolution 1.68 Å R-free 0.236
6OI2 Crystal structure of human WDR5 in complex with symmetric dimethyl-L-arginine Deposited 2019-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded SO4 SULFATE ION × 3 GOL GLYCEROL × 3 2MR N3, N4-DIMETHYLARGININE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；295 K；100 mM Bis-Tris pH5.9, 32% PEG3350, 54.6 mM Ammonium Sulfate, 0.66 mM symmetric dimethyl-L-arginine
Resolution 1.68 Å R-free 0.223
6OI3 Crystal structure of human WDR5 in complex with monomethyl H3R2 peptide Deposited 2019-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded GOL GLYCEROL × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；295 K；100 mM Bis-Tris pH 5.9, 32% PEG3350, 54.6 mM Ammonium Sulfate, 1.67 mM monomethyl H3R2 peptide
Resolution 1.66 Å R-free 0.202
6PG3 WDR5delta23 bound to (2-butyl-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded OHJ (2-butyl-1H-imidazol-4-yl)methanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.182 M ammonium fluoride, 0.1 M sodium cacodylate (pH 5.79), 22.1 %w/v PEG8000
Resolution 2.04 Å R-free 0.206
6PG3 WDR5delta23 bound to (2-butyl-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded OHJ (2-butyl-1H-imidazol-4-yl)methanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.182 M ammonium fluoride, 0.1 M sodium cacodylate (pH 5.79), 22.1 %w/v PEG8000
Resolution 2.04 Å R-free 0.206
6PG4 WDR5delta32 bound to (2-methyl-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa）
Not recorded OHG (2-methyl-1H-imidazol-4-yl)methanol × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.114 M ammonium sulfate, 0.1 M bis-tris chloride (pH 6.11), 25.8 %w/v PEG8000
Resolution 1.60 Å R-free 0.176
6PG5 WDR5delta32 bound to benzyl (4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)carbamate Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa）
Not recorded OHV benzyl {4-[5-(hydroxymethyl)-1H-imidazol-2-yl]butyl}carbamate × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.215 M ammonium sulfate, 0.1 M sodium cacodylate (pH 7.06), 25.6 %w/v PEG8000
Resolution 1.99 Å R-free 0.202
6PG6 WDR5delta23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)acetamide Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded SO4 SULFATE ION × 1 OH7 N-{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}acetamide × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.215 M ammonium sulfate, 0.1 M sodium cacodylate (pH 7.06), 25.6 %w/v PEG8000
Resolution 1.68 Å R-free 0.193
6PG6 WDR5delta23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)acetamide Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded SO4 SULFATE ION × 1 OH7 N-{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.215 M ammonium sulfate, 0.1 M sodium cacodylate (pH 7.06), 25.6 %w/v PEG8000
Resolution 1.68 Å R-free 0.193
6PG7 WDR5delta32 bound to (2-(3-methoxy-3-phenylpropyl)-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa）
Not recorded OH4 {2-[(3S)-3-methoxy-3-phenylpropyl]-1H-imidazol-4-yl}methanol × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.17 M ammonium sulfate, 0.1 bis-tris chloride (pH 6.3), 30.5 %w/v PEG4000
Resolution 2.45 Å R-free 0.243
6PG8 WDR5delta23 bound to (2-(3-phenylpropyl)-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded OGY [2-(3-phenylpropyl)-1H-imidazol-4-yl]methanol × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.179 M ammonium sulfate, 0.1 M bis-tris chloride (pH 5.62), 28.6 %w/v PEG3350
Resolution 1.67 Å R-free 0.207
6PG8 WDR5delta23 bound to (2-(3-phenylpropyl)-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded OGY [2-(3-phenylpropyl)-1H-imidazol-4-yl]methanol × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.179 M ammonium sulfate, 0.1 M bis-tris chloride (pH 5.62), 28.6 %w/v PEG3350
Resolution 1.67 Å R-free 0.207
6PG8 WDR5delta23 bound to (2-(3-phenylpropyl)-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 22–334（313 aa）
Not recorded OGY [2-(3-phenylpropyl)-1H-imidazol-4-yl]methanol × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.179 M ammonium sulfate, 0.1 M bis-tris chloride (pH 5.62), 28.6 %w/v PEG3350
Resolution 1.67 Å R-free 0.207
6PG8 WDR5delta23 bound to (2-(3-phenylpropyl)-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 22–334（313 aa）
Not recorded OGY [2-(3-phenylpropyl)-1H-imidazol-4-yl]methanol × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.179 M ammonium sulfate, 0.1 M bis-tris chloride (pH 5.62), 28.6 %w/v PEG3350
Resolution 1.67 Å R-free 0.207
6PG9 WDR5delta23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)benzamide Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded OH1 N-{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.182 M ammonium fluoride, 0.1 soidum cacodylate (pH 5.79), 22.1 %w/v PEG8000
Resolution 1.75 Å R-free 0.269
6PG9 WDR5delta23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)benzamide Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded OH1 N-{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.182 M ammonium fluoride, 0.1 soidum cacodylate (pH 5.79), 22.1 %w/v PEG8000
Resolution 1.75 Å R-free 0.269
6PGA WDR5delta32 bound to methyl (4-(4-(hydroxymethyl)-1H-imidazol-2-yl)butyl)carbamate Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa）
Not recorded OGM methyl {4-[5-(hydroxymethyl)-1H-imidazol-2-yl]butyl}carbamate × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.237 M ammonium sulfate, 0.1 M bis-tris chloride, 25.7 %w/v MPEG5000
Resolution 2.45 Å R-free 0.250
6PGB WDR5delta32 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)-2-phenylacetamide Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa） Fragment：UNP residues 32-334
Not recorded OJG N-{4-[5-(hydroxymethyl)-1H-imidazol-2-yl]butyl}-2-phenylacetamide × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.101 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 5.63, 25.8% w/v PEG4000
Resolution 1.73 Å R-free 0.217
6PGC WDR5delta32 bound to methyl benzyl(4-(4-(hydroxymethyl)-1H-imidazol-2-yl)butyl)carbamate Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa） Fragment：UNP residues 32-334
Not recorded SO4 SULFATE ION × 2 OJJ methyl benzyl{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}carbamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.237 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 6.92, 25.7% w/v MPEG5000
Resolution 1.81 Å R-free 0.248
6PGD WDR5delta32 bound to peptidomimetic Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa） Fragment：UNP residues 32-334
Not recorded OK4 N-acetyl-L-alanyl-5-[5-(hydroxymethyl)-1H-imidazol-2-yl]-L-norvalyl-L-valinamide × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.233 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 6.02, 26% w/v PEG8000
Resolution 1.50 Å R-free 0.167
6PGE WDR5delta32 bound to ethyl 3-(4-(hydroxymethyl)-1H-imidazol-2-yl)propanoate Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa） Fragment：UNP residues 32-334
Not recorded OJM ethyl 3-[4-(hydroxymethyl)-1H-imidazol-2-yl]propanoate × 1 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.024 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 5.64, 26.3% w/v PEG4000
Resolution 1.76 Å R-free 0.213
6PGF WDR5delta32 bound to N-(4-(4-(hydroxymethyl)-1H-imidazol-2-yl)butyl)acrylamide Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa） Fragment：UNP residues 32-334
Not recorded OJP N-{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}prop-2-enamide × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.16 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 6.1, 30.1% w/v PEG8000
Resolution 1.54 Å R-free 0.170
6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain B 22–334（313 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
6PWW Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome Deposited 2019-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 22–334（313 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6U5M Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q0S 5-bromo-2-hydroxy-N-[3-(methylsulfonyl)-5-(pentafluoro-lambda~6~-sulfanyl)phenyl]benzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, ammonium acetate, PEG 3350
Resolution 1.80 Å R-free 0.186
6U5M Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q0S 5-bromo-2-hydroxy-N-[3-(methylsulfonyl)-5-(pentafluoro-lambda~6~-sulfanyl)phenyl]benzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, ammonium acetate, PEG 3350
Resolution 1.80 Å R-free 0.186
6U5Y Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q0M 3-{[(5-bromo-3-chloro-2-hydroxyphenyl)sulfonyl]amino}-5-(1-cyanocyclobutyl)-2-hydroxy-N-methylbenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris pH 6.5, 0.2 M ammonium acetate, 28% PEG 3350
Resolution 1.53 Å R-free 0.177
6U5Y Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q0M 3-{[(5-bromo-3-chloro-2-hydroxyphenyl)sulfonyl]amino}-5-(1-cyanocyclobutyl)-2-hydroxy-N-methylbenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris pH 6.5, 0.2 M ammonium acetate, 28% PEG 3350
Resolution 1.53 Å R-free 0.177
6U6W Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded Q0Y 5-bromo-N-(5-chloro-2-hydroxyphenyl)-2-methoxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris pH 6.5, 0.2M ammonium acetate, PEG3350
Resolution 1.20 Å R-free 0.179
6U6W Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa）
Not recorded Q0Y 5-bromo-N-(5-chloro-2-hydroxyphenyl)-2-methoxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris pH 6.5, 0.2M ammonium acetate, PEG3350
Resolution 1.20 Å R-free 0.179
6U80 Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded Q1J 5-bromo-N-(4-hydroxy[1,1'-biphenyl]-3-yl)-2-methoxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium Acetate, PEG 3350
Resolution 1.55 Å R-free 0.203
6U80 Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa）
Not recorded Q1J 5-bromo-N-(4-hydroxy[1,1'-biphenyl]-3-yl)-2-methoxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium Acetate, PEG 3350
Resolution 1.55 Å R-free 0.203
6U8B Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded Q1M 3-{[(5-bromo-2-methoxyphenyl)sulfonyl]amino}-5-chloro-2-hydroxybenzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, ammonium acetate, PEG 3350
Resolution 1.26 Å R-free 0.159
6U8B Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa）
Not recorded Q1M 3-{[(5-bromo-2-methoxyphenyl)sulfonyl]amino}-5-chloro-2-hydroxybenzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, ammonium acetate, PEG 3350
Resolution 1.26 Å R-free 0.159
6U8L Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q1P 3-{[(5-bromo-2-hydroxyphenyl)sulfonyl]amino}-5-cyclopropyl-6-fluoro-2-hydroxybenzoic acid × 1 Q1S N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]isoquinolin-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium acetate, PEG 3350
Resolution 1.57 Å R-free 0.176
6U8L Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q1P 3-{[(5-bromo-2-hydroxyphenyl)sulfonyl]amino}-5-cyclopropyl-6-fluoro-2-hydroxybenzoic acid × 1 Q1S N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]isoquinolin-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium acetate, PEG 3350
Resolution 1.57 Å R-free 0.176
6U8O Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q1G 5-bromo-N-[5-(1-cyanocyclobutyl)-2-hydroxyphenyl]-2-hydroxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, ammonium acetate, PEG 3350
Resolution 1.60 Å R-free 0.184
6UCS Discovery and Structure-Based optimization of potent and selective WDR5 inhibitors containing a dihydroisoquinolinone bicyclic core Deposited 2019-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded Q41 2-amino-3-{[(5P)-2-[(3,5-dimethoxyphenyl)methyl]-5-(4-fluoro-2-methylphenyl)-1-oxo-1,2,3,4-tetrahydroisoquinolin-7-yl]methyl}-1-methyl-1H-imidazol-3-ium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium Acetate, PEG 3350
Resolution 1.85 Å R-free 0.194
6UCS Discovery and Structure-Based optimization of potent and selective WDR5 inhibitors containing a dihydroisoquinolinone bicyclic core Deposited 2019-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded Q41 2-amino-3-{[(5P)-2-[(3,5-dimethoxyphenyl)methyl]-5-(4-fluoro-2-methylphenyl)-1-oxo-1,2,3,4-tetrahydroisoquinolin-7-yl]methyl}-1-methyl-1H-imidazol-3-ium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium Acetate, PEG 3350
Resolution 1.85 Å R-free 0.194
6UFX WD repeat-containing protein 5 complexed with N-[(3,5-dimethoxyphenyl)methyl]-4'-fluoro-5-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}-2'-methyl[1,1'-biphenyl]-3-carboxamide (compound 13) Deposited 2019-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa） Fragment：UNP residues 32-334
Not recorded Q6S N-[(3,5-dimethoxyphenyl)methyl]-4'-fluoro-5-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}-2'-methyl[1,1'-biphenyl]-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Bis-Tris or HEPES or Tris-HCl, pH 6.0-8.0, 0.2 M ammonium acetate, 20-30% PEG3350
Resolution 2.02 Å R-free 0.208
6UHY WDR5 in complex with Myc site fragment inhibitor Deposited 2019-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q8G 1-cyclohexyl-1H-benzimidazole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350.
Resolution 1.26 Å R-free 0.181
6UHY WDR5 in complex with Myc site fragment inhibitor Deposited 2019-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q8G 1-cyclohexyl-1H-benzimidazole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350.
Resolution 1.26 Å R-free 0.181
6UHZ WDR5 in complex with Myc site fragment inhibitor Deposited 2019-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q8D 1-cyclohexyl-1H-benzotriazole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% PEG3350
Resolution 1.26 Å R-free 0.176
6UHZ WDR5 in complex with Myc site fragment inhibitor Deposited 2019-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q8D 1-cyclohexyl-1H-benzotriazole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% PEG3350
Resolution 1.26 Å R-free 0.176
6UIF Discovery of fragment-inspired heterocyclic benzenesulfonmides as inhibitors of the WDR5-MYC interaction Deposited 2019-09-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q8P 4-{[(5-bromo-3-chloro-2-hydroxyphenyl)sulfonyl]amino}-1-cyclopentyl-N-methyl-1H-imidazole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium acetate, PEG 3350
Resolution 1.60 Å R-free 0.194
6UIF Discovery of fragment-inspired heterocyclic benzenesulfonmides as inhibitors of the WDR5-MYC interaction Deposited 2019-09-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q8P 4-{[(5-bromo-3-chloro-2-hydroxyphenyl)sulfonyl]amino}-1-cyclopentyl-N-methyl-1H-imidazole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium acetate, PEG 3350
Resolution 1.60 Å R-free 0.194
6UIK Discovery of fragment-inspired heterocyclic benzenesulfonmides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q8M 5-bromo-3-chloro-N-(1-cyclopentyl-1H-imidazol-4-yl)-2-hydroxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris 6.5, 0.2 M Ammonium Acetate, 28% PEG 3350
Resolution 1.60 Å R-free 0.182
6UIK Discovery of fragment-inspired heterocyclic benzenesulfonmides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q8M 5-bromo-3-chloro-N-(1-cyclopentyl-1H-imidazol-4-yl)-2-hydroxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris 6.5, 0.2 M Ammonium Acetate, 28% PEG 3350
Resolution 1.60 Å R-free 0.182
6UJ4 Discovery of fragment-inspired heterocyclic benzenesulfonmides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q8S 5-bromo-3-chloro-N-(1-cyclopentyl-2-methyl-1H-imidazol-4-yl)-2-hydroxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris 6.5, 0.2 M Ammonium acetate, 28% PEG 3350
Resolution 1.53 Å R-free 0.177
6UJ4 Discovery of fragment-inspired heterocyclic benzenesulfonmides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q8S 5-bromo-3-chloro-N-(1-cyclopentyl-2-methyl-1H-imidazol-4-yl)-2-hydroxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris 6.5, 0.2 M Ammonium acetate, 28% PEG 3350
Resolution 1.53 Å R-free 0.177
6UJH Discovery of fragment-inspired heterocyclic benzenesulfonamides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded QBS (2R)-2-(4-chlorophenyl)-3-oxobutanenitrile × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes, 0.2 M ammonium acetate, 32% PEG3350
Resolution 1.49 Å R-free 0.169
6UJH Discovery of fragment-inspired heterocyclic benzenesulfonamides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded QBS (2R)-2-(4-chlorophenyl)-3-oxobutanenitrile × 1 SO4 SULFATE ION × 1 DMS DIMETHYL SULFOXIDE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes, 0.2 M ammonium acetate, 32% PEG3350
Resolution 1.49 Å R-free 0.169
6UJJ Discovery of fragment-inspired heterocyclic benzenesulfonamides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded QBP 5-[4-(trifluoromethyl)phenyl]-1H-tetrazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Hepes, 0.2 M ammonium acetate, 32% PEG3350
Resolution 1.73 Å R-free 0.190
6UJL Discovery of fragment-inspired heterocyclic benzenesulfonamides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded QBM 6-methyl-3-(propylsulfanyl)-1,2,4-triazin-5-ol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Hepes, 0.2 M ammonium acetate, 32% PEG3350
Resolution 1.60 Å R-free 0.183
6UOZ Discovery of fragment-inspired heterocyclic benzenesulfonmides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–334（304 aa）
Chain B 31–334（304 aa）
Not recorded QF1 5-bromo-3-chloro-N-[1-cyclopentyl-2-(methylsulfonyl)-1H-imidazol-4-yl]-2-hydroxybenzene-1-sulfonamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, ammonium acetate, PEG 3350
Resolution 1.53 Å R-free 0.169
6W5I Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class01) Deposited 2020-03-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 22–334（313 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 22–334（313 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6W5N Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Deposited 2020-03-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 22–334（313 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
6WJQ Crystal structure of WDR5 in complex with the WIN peptide of PDPK1 Deposited 2020-04-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；PEG 3350, Ammonium Acetate, Bis-tris
Resolution 2.71 Å R-free 0.252
6WJQ Crystal structure of WDR5 in complex with the WIN peptide of PDPK1 Deposited 2020-04-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；PEG 3350, Ammonium Acetate, Bis-tris
Resolution 2.71 Å R-free 0.252
7AXP Structural characterisation of WDR5:CS-VIP8 interaction in cis state 2 Deposited 2020-11-10 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate
Resolution 2.43 Å R-free 0.331
7AXQ Structure of the cryo-trapped WDR5:CS-VIP8 cocrystal after illumination at 405 nm and 180 K Deposited 2020-11-10 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate
Resolution 1.56 Å R-free 0.200
7AXS Structural characterisation of WDR5:CS-VIP8 interaction in cis state 1 Deposited 2020-11-10 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate
Resolution 1.88 Å R-free 0.235
7AXU Structure of WDR5:CS-VIP8 cocrystal after illumination in situ Deposited 2020-11-10 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate
Resolution 1.68 Å R-free 0.193
7AXX Structure of WDR5:CS-VIP8 crystal after illumination at 405 nm and room temperature Deposited 2020-11-10 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate
Resolution 1.79 Å R-free 0.214
7BCY X-ray structure of WDR5delta24 bound to the Kaposi's sarcoma herpesvirus LANA win motif peptide Deposited 2020-12-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 25–334（310 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；294 K；100 mM Bis-Tris pH 5.5, 50 mM (NH4)2SO4, 25% PEG3350
Resolution 1.50 Å R-free 0.227
7BCY X-ray structure of WDR5delta24 bound to the Kaposi's sarcoma herpesvirus LANA win motif peptide Deposited 2020-12-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 25–334（310 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；294 K；100 mM Bis-Tris pH 5.5, 50 mM (NH4)2SO4, 25% PEG3350
Resolution 1.50 Å R-free 0.227
7BED X-ray structure of WDR5 bound to the WDR5 win motif peptide Deposited 2020-12-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Chain B 1–334（334 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；26% PEG 3350, 100mM Bis-Tris pH 5.5, 50mM (NH4)2SO4,WDR5 at 14,65 mg/ml with 2:1 (protein:well) drop ratio.
Resolution 1.26 Å R-free 0.171
7CFP Crystal structure of WDR5 in complex with a H3Q5ser peptide Deposited 2020-06-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Not recorded SRO SEROTONIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；0.1% Octylglucoside, 0.1M Sodium citrate tribasic dihydrate pH 5.5, 22% PEG 3350
Resolution 1.60 Å R-free 0.199
7CFQ Crystal structure of WDR5 in complex with H3K4me3Q5ser peptide Deposited 2020-06-27 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Not recorded GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1 SRO SEROTONIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；0.15M ammonium sulfate, 0.1M MES pH 5.5, 25% PEG 4000, 2% PEG 3350
Resolution 1.60 Å R-free 0.190
7DNO Characterization of Peptide Ligands Against WDR5 Isolated Using Phage Display Technique Deposited 2020-12-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 24–334（311 aa）
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1 M BisTris pH 6.0, 0.2M ammonium acetate, 20-30% PEG3350
Resolution 2.03 Å R-free 0.227
7JTO Crystal structure of Protac MS33 in complex with the WD repeat-containing protein 5 and pVHL:ElonginC:ElonginB Deposited 2020-08-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 31–334（304 aa）
Not recorded SCN THIOCYANATE ION × 4 EDO 1,2-ETHANEDIOL × 5 VKA 3-methyl-N-(11-{[2-(4-{[4'-(4-methylpiperazin-1-yl)-3'-{[6-oxo-4-(trifluoromethyl)-5,6-dihydropyridine-3-carbonyl]amino}[1,1'-biphenyl]-3-yl]methyl}piperazin-1-yl)ethyl]amino}-11-oxoundecanoyl)-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 GOL GLYCEROL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.1 M HEPES sodium, pH 7.5-8.0, 1.3-1.6 M sodium thiocyanate, 15-20% PEG3350
Resolution 1.70 Å R-free 0.225
7JTP Crystal structure of Protac MS67 in complex with the WD repeat-containing protein 5 and pVHL:ElonginC:ElonginB Deposited 2020-08-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 31–334（304 aa）
Not recorded GOL GLYCEROL × 1 X6M N-(6-fluoro-3'-{[6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carbonyl]amino}-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-carbonyl)glycyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.1 M Tris, pH 8.5, 30% PEG300
Resolution 2.12 Å R-free 0.224
7MBM Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Deposited 2021-04-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 22–334（313 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.76 Å
7MBN Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Deposited 2021-04-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 22–334（313 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
7Q2J Quaternary Complex of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC Homer Deposited 2021-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 24–334（311 aa）
Not recorded 8KH N-[5-[4-[[5-[[(2S)-3,3-dimethyl-1-[(2S,4R)-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-5-oxidanylidene-pentyl]carbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanylidene-4-(trifluoromethyl)-1H-pyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；21% PEG 3350 0.4 M KSCN 0.1 M HEPES 6.8
Resolution 2.50 Å R-free 0.293
7U9Y WDR5 bound to 2-(3,5-dimethoxybenzyl)-7-((2-methyl-1H-imidazol-1-yl)methyl)-5-(1-methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl)-3,4-dihydroisoquinolin-1(2H)-one Deposited 2022-03-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 30–334（305 aa）
Not recorded BEN BENZAMIDINE × 1 M4U (5P)-2-[(3,5-dimethoxyphenyl)methyl]-7-[(2-methyl-1H-imidazol-1-yl)methyl]-5-[1-methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-3,4-dihydroisoquinolin-1(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；BIS-Tris, ammonium acetate, PEG 3350, benzamidine
Resolution 1.90 Å R-free 0.189
7UAS Discovery of Potent Orally Bioavailable WD Repeat Domain 5 (WDR5) Inhibitors Using a Pharmacophore-Based Optimization Deposited 2022-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded MBU (5P)-2-[(S)-cyclopropyl(4-methylpyridin-2-yl)methyl]-5-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-7-[(2-methyl-1H-imidazol-1-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium Acetate, PEG 3350
Resolution 1.81 Å R-free 0.175
7UAS Discovery of Potent Orally Bioavailable WD Repeat Domain 5 (WDR5) Inhibitors Using a Pharmacophore-Based Optimization Deposited 2022-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded MBU (5P)-2-[(S)-cyclopropyl(4-methylpyridin-2-yl)methyl]-5-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-7-[(2-methyl-1H-imidazol-1-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium Acetate, PEG 3350
Resolution 1.81 Å R-free 0.175
7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain L 2–334（333 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
7WVK Crystal structure of human WDR5 in complex with compound 19 Deposited 2022-02-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded 6IQ 1-[2,5-bis(chloranyl)phenyl]sulfonylbenzimidazole × 1 GOL GLYCEROL × 4 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1M Bis-Tris, 0.2 M NH4OAC, 30% PEG3350
Resolution 1.42 Å R-free 0.182
8BB2 Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #2) Deposited 2022-10-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 33–334（302 aa）
Not recorded SCN THIOCYANATE ION × 5 Q3X ~{N}-[5-[4-[2-[2-[2-[2-[3-[[3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanylidene-4-(trifluoromethyl)-3~{H}-pyridine-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；21-28% PEG 3350 0.4-1 M KSCN 0.1 M HEPES 6.8
Resolution 2.05 Å R-free 0.237
8BB3 Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #1) Deposited 2022-10-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 33–334（302 aa）
Not recorded SCN THIOCYANATE ION × 15 EDO 1,2-ETHANEDIOL × 13 P6G HEXAETHYLENE GLYCOL × 1 Q3X ~{N}-[5-[4-[2-[2-[2-[2-[3-[[3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanylidene-4-(trifluoromethyl)-3~{H}-pyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；21-26% PEG 3350 0.4-1 M KSCN 0.1 M HEPES
Resolution 1.80 Å R-free 0.227
8BB4 Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with C3 linker Deposited 2022-10-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain Q 33–334（302 aa）
Not recorded Q3R ~{N}-[5-[4-[[4-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-4-oxidanylidene-butyl]carbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanyl-4-(trifluoromethyl)pyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；21-28% PEG 3350 0.4 M KSCN 0.1 M HEPES pH 6.8
Resolution 2.80 Å R-free 0.279
8BB5 Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with Aryl linker Deposited 2022-10-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 33–334（302 aa）
Not recorded SCN THIOCYANATE ION × 10 Q43 ~{N}-[5-[4-[[4-[2-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-2-oxidanylidene-ethyl]phenyl]methylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanyl-4-(trifluoromethyl)pyridine-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 4 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；21% PEG 3350, 0.4-1 M KSCN 0.1 M HEPES pH 6.8
Resolution 2.20 Å R-free 0.248
8DU4 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Deposited 2022-07-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain L 2–334（333 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
8E9F WD repeat-containing protein 5 complexed with 4-(7-((1H-imidazol-1-yl)methyl)-5-(1-methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl)-1-oxo-3,4-dihydroisoquinolin-2(1H)-yl)-6-ethyl-N-methylquinoline-8-carboxamide (compound 10) Deposited 2022-08-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 30–334（305 aa）
Not recorded BEN BENZAMIDINE × 1 UY9 6-ethyl-4-[(5P)-7-[(1H-imidazol-1-yl)methyl]-5-[1-methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-1-oxo-3,4-dihydroisoquinolin-2(1H)-yl]-N-methylquinoline-8-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；BIS-Tris, ammonium acetate, PEG 3350, benzamidine
Resolution 1.55 Å R-free 0.184
8F1G Crystal structure of human WDR5 in complex with compound WM662 Deposited 2022-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded X8N (2S)-2-({(2S)-3-(3'-chloro[1,1'-biphenyl]-4-yl)-1-oxo-1-[(1H-tetrazol-5-yl)amino]propan-2-yl}oxy)propanoic acid × 1 GOL GLYCEROL × 4 SO4 SULFATE ION × 1 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH=7.4, 25 mM ammonium sulfate, 24% w/v Polyethylene glycol 3350
Resolution 2.14 Å R-free 0.249
8F1G Crystal structure of human WDR5 in complex with compound WM662 Deposited 2022-11-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded X8N (2S)-2-({(2S)-3-(3'-chloro[1,1'-biphenyl]-4-yl)-1-oxo-1-[(1H-tetrazol-5-yl)amino]propan-2-yl}oxy)propanoic acid × 1 GOL GLYCEROL × 3 SO4 SULFATE ION × 1 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH=7.4, 25 mM ammonium sulfate, 24% w/v Polyethylene glycol 3350
Resolution 2.14 Å R-free 0.249
8F93 WDR5 covalently modified at Y228 by (R)-2-SF Deposited 2022-11-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: monomeric
Chain A 22–334（313 aa）
Chain B 22–334（313 aa）
Not recorded XKN 3-ethynyl-5-{[(3R)-4-{1-[(2-methoxyphenyl)methyl]-1H-benzimidazole-5-carbonyl}-3-methylpiperazin-1-yl]methyl}benzene-1-sulfonyl fluoride × 2 GOL GLYCEROL × 4 SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium sulfate, 0.1 M MES pH 6.5, 20% w/v PEG 8000
Resolution 2.30 Å R-free 0.253
8F93 WDR5 covalently modified at Y228 by (R)-2-SF Deposited 2022-11-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: monomeric
Chain A 22–334（313 aa）
Chain B 22–334（313 aa）
Not recorded XKN 3-ethynyl-5-{[(3R)-4-{1-[(2-methoxyphenyl)methyl]-1H-benzimidazole-5-carbonyl}-3-methylpiperazin-1-yl]methyl}benzene-1-sulfonyl fluoride × 2 GOL GLYCEROL × 4 SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium sulfate, 0.1 M MES pH 6.5, 20% w/v PEG 8000
Resolution 2.30 Å R-free 0.253
8G3C Crystal structure of human WDR5 in complex with N-[(2'-cyano[1,1'-biphenyl]-4-yl)methyl]-3-hydroxy-6-methyl-4-oxo-4H-pyran-2-carboxamide (compound 1, WDR5-MYC PPI inhibitor) Deposited 2023-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded YJN N-[(2'-cyano[1,1'-biphenyl]-4-yl)methyl]-3-hydroxy-6-methyl-4-oxo-4H-pyran-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；20% PEG3350, 0.2 M potassium acetate
Resolution 1.80 Å R-free 0.224
8G3E Crystal structure of human WDR5 in complex with (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide (compound 2, WDR5-MYC inhibitor) Deposited 2023-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded YJR (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；23.5% PEG3350, 0.21 M ammonium sulfate, 0.1 M HEPES, pH 7.5
Resolution 1.33 Å R-free 0.170
8G3E Crystal structure of human WDR5 in complex with (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide (compound 2, WDR5-MYC inhibitor) Deposited 2023-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded YJR (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；23.5% PEG3350, 0.21 M ammonium sulfate, 0.1 M HEPES, pH 7.5
Resolution 1.33 Å R-free 0.170
8HMX WDR5 in complex with histone H3Q5his peptide Deposited 2022-12-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 31–334（304 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium citrate tribasic dihydrate (pH 5.5), 22% polyethylene glycol (PEG) 3350, and 0.1% n-Octyl-beta-D-glucoside
Resolution 1.70 Å R-free 0.193
8Q1N Cyclic peptide binder of the WBM-site of WDR5 Deposited 2023-08-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Li3-Citrate, 20 w/v% PEG3350
Resolution 1.84 Å R-free 0.243
8Q1N Cyclic peptide binder of the WBM-site of WDR5 Deposited 2023-08-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Li3-Citrate, 20 w/v% PEG3350
Resolution 1.84 Å R-free 0.243
8T5I Crystal structure of human WDR5 in complex with MR4397 Deposited 2023-06-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded ZHF N-[(2S)-1-(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)-1-oxopentan-2-yl]-3-[(1H-imidazol-1-yl)methyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 3 UNX UNKNOWN LIGAND × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；25% PEG3350, 0.2 M (NH4)2SO4, 0.1M BTP pH 7.0
Resolution 1.70 Å R-free 0.232
8T5I Crystal structure of human WDR5 in complex with MR4397 Deposited 2023-06-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded ZHF N-[(2S)-1-(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)-1-oxopentan-2-yl]-3-[(1H-imidazol-1-yl)methyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 5 UNX UNKNOWN LIGAND × 1 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；25% PEG3350, 0.2 M (NH4)2SO4, 0.1M BTP pH 7.0
Resolution 1.70 Å R-free 0.232
8UJY Crystal structure of human WD repeat-containing protein 5 in complex with 4-(3,5-dimethoxybenzyl)-9-(4-fluoro-2-methylphenyl)-7-((2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl)methyl)-3,4-dihydrobenzo[f][1,4]oxazepin-5(2H)-one (compound 8) Deposited 2023-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa） Fragment：UNP residues 23-334
Chain B 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded VV3 (9P)-4-[(3,5-dimethoxyphenyl)methyl]-9-(4-fluoro-2-methylphenyl)-7-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}-3,4-dihydro-1,4-benzoxazepin-5(2H)-one × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1 M Bis-Tris pH 7.0, 0.2 M ammonium acetate, 25% PEG3350
Resolution 2.01 Å R-free 0.232
8WXQ Structure of WDR5 in complex with WIN motif containing MBD3C Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M HEPES (pH 7.5), 18% PEG 600
Resolution 1.90 Å R-free 0.209
8WXQ Structure of WDR5 in complex with WIN motif containing MBD3C Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M HEPES (pH 7.5), 18% PEG 600
Resolution 1.90 Å R-free 0.209
8WXR Structure of WDR5 in complex with WIN motif containing MBD3C F47A Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M potassium dihydrogen phosphate, 20% PEG 3350
Resolution 2.08 Å R-free 0.199
8WXR Structure of WDR5 in complex with WIN motif containing MBD3C F47A Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M potassium dihydrogen phosphate, 20% PEG 3350
Resolution 2.08 Å R-free 0.199
8WXT Structure of WDR5 in complex with WIN motif containing MBD3C R45E/V46G Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.2 M imidazole malate, pH 5.5, 33% PEG 600
Resolution 1.83 Å R-free 0.179
8WXU Structure of WDR5 in complex with WIN motif containing MBD3C C44S/R45E/V46G Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M lithium chloride, 20% PEG 3350
Resolution 2.37 Å R-free 0.233
8WXV Structure of WDR5 in complex with WIN motif containing SET1B Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.1 M Bis-Tris, pH 5.5, 25% PEG 3350
Resolution 2.40 Å R-free 0.205
8WXV Structure of WDR5 in complex with WIN motif containing SET1B Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.1 M Bis-Tris, pH 5.5, 25% PEG 3350
Resolution 2.40 Å R-free 0.205
8WXX Structure of WDR5 in complex with WIN motif containing SET1B E1750R/G1751V Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.1 M sodium citrate, pH 5.5, 16% PEG 4000, 10% 2-propanol
Resolution 2.10 Å R-free 0.212
8WXX Structure of WDR5 in complex with WIN motif containing SET1B E1750R/G1751V Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.1 M sodium citrate, pH 5.5, 16% PEG 4000, 10% 2-propanol
Resolution 2.10 Å R-free 0.212
8X3R Crystal structure of human WDR5 in complex with WDR5 Deposited 2023-11-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Chain B 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M magnesium formate dihydrate, 15% w/v polyethylene glycol 3350
Resolution 1.76 Å R-free 0.205
8X3S Crystal structure of human WDR5 in complex with PTEN Deposited 2023-11-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M lithium sulfate monohydrate, 0.1 M HEPES at pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 1.87 Å R-free 0.259
9B9H Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40333 Deposited 2024-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded A1AM2 N-{(1P)-5'-({(17E)-18-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-16-oxo-3,6,9,12-tetraoxa-15-azaoctadec-17-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；5% w/v 1-ethyl-3-methylimidazolium ethyl sulfate, 15% w/v polyethylene glycol 20,000, pH 7.9
Resolution 2.06 Å R-free 0.229
9B9T Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40407 Deposited 2024-04-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded A1ANM N-{(1P)-5'-[(17-{(4P)-4-[(2P)-4-{[(1R)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-1H-pyrazol-1-yl}-16-oxo-3,6,9,12-tetraoxa-15-azaheptadecan-1-yl)carbamoyl]-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate trihydrate, pH 4.6, 2.0 M sodium formate
Resolution 2.05 Å R-free 0.196
9B9W Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40792 Deposited 2024-04-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded A1ANN (4P)-N-[(1R)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(25E)-1-{(1P)-6-fluoro-3'-[4-fluoro-2-(trifluoromethyl)benzamido]-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-1,24-dioxo-5,8,11,14,17,20-hexaoxa-2,23-diazahexacos-25-en-26-yl]-1H-pyrrole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；35% v/v tacsimate, pH 7.0
Resolution 1.92 Å R-free 0.183
9BA2 Crystal structure of the binary complex of DCAF1 and WDR5 Deposited 2024-04-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded IMD IMIDAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.2 M imidazole, pH 7.4, 20% w/v polyethylene glycol 4,000
Resolution 2.97 Å R-free 0.266
9D5Z Crystal structure of the human WDR5 in complex with LH168 compound Deposited 2024-08-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded A1A16 (3P)-N-[(2S)-1-(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)-1-oxopentan-2-yl]-3-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-5-[(1H-imidazol-1-yl)methyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M Ammonium formate
Resolution 1.70 Å R-free 0.189
9D5Z Crystal structure of the human WDR5 in complex with LH168 compound Deposited 2024-08-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded A1A16 (3P)-N-[(2S)-1-(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)-1-oxopentan-2-yl]-3-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-5-[(1H-imidazol-1-yl)methyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M Ammonium formate
Resolution 1.70 Å R-free 0.189
9DLW Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41114 Deposited 2024-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded A1BAF N-{(1P)-5'-({(32E)-33-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-31-oxo-3,6,9,12,15,18,21,24,27-nonaoxa-30-azatritriacont-32-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；294 K；1.8 M Sodium phosphate monobasic monohydrate, potassium phosphate dibasic / pH 6.9
Resolution 2.07 Å R-free 0.242
9IY5 WDR5 inhibitor complex Deposited 2024-07-30 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；Bis-tris pH 5.5 25% PEG 4000
Resolution 1.80 Å R-free 0.255
9IY5 WDR5 inhibitor complex Deposited 2024-07-30 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；Bis-tris pH 5.5 25% PEG 4000
Resolution 1.80 Å R-free 0.255
9J20 Structure of WDR5 in complex with KIF2A Deposited 2024-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M HEPES (pH 7.5) and 18% PEG 600
Resolution 1.85 Å R-free 0.206
9J20 Structure of WDR5 in complex with KIF2A Deposited 2024-08-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M HEPES (pH 7.5) and 18% PEG 600
Resolution 1.85 Å R-free 0.206
9JWV Structure of WDR5 Y191F in complex with WIN motif containing Kif2A Deposited 2024-10-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Mutation：Y191F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M HEPES (pH 7.5), 18% PEG 600
Resolution 1.80 Å R-free 0.211
9JWV Structure of WDR5 Y191F in complex with WIN motif containing Kif2A Deposited 2024-10-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Mutation：Y191F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M HEPES (pH 7.5), 18% PEG 600
Resolution 1.80 Å R-free 0.211
9KD4 Structure of WDR5 in complex with WIN motif containing Kif2A 114-120 Deposited 2024-11-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium acetate, 0.1 M Sodium acetate pH=4, 15% PEG 4000
Resolution 1.64 Å R-free 0.204
9KD4 Structure of WDR5 in complex with WIN motif containing Kif2A 114-120 Deposited 2024-11-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium acetate, 0.1 M Sodium acetate pH=4, 15% PEG 4000
Resolution 1.64 Å R-free 0.204
9KD5 Structure of WDR5 in complex with WIN motif containing Kif2A S121G Deposited 2024-11-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M imidazole malate, pH=5.5, 24% PEG 600
Resolution 1.80 Å R-free 0.216
9KD5 Structure of WDR5 in complex with WIN motif containing Kif2A S121G Deposited 2024-11-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M imidazole malate, pH=5.5, 24% PEG 600
Resolution 1.80 Å R-free 0.216
9KFM Structure of WDR5 in complex with WIN motif containing EMBOW Deposited 2024-11-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium cacodylate, pH 5.5, 25% (w/v) PEG 4000
Resolution 1.80 Å R-free 0.201
9KFM Structure of WDR5 in complex with WIN motif containing EMBOW Deposited 2024-11-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium cacodylate, pH 5.5, 25% (w/v) PEG 4000
Resolution 1.80 Å R-free 0.201
9KFN Structure of WDR5 in complex with mutated EMBOW T3V Deposited 2024-11-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M imidazole malate, pH 8.5, 12.5 % (w/v) PEG 10000.
Resolution 2.80 Å R-free 0.241
9KFO Structure of WDR5 in complex with mutated EMBOW Deposited 2024-11-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium HEPES, pH 7.0, 15 % (w/v) PEG 4000.
Resolution 2.20 Å R-free 0.190
9KQS Crystal structure of WDR5 in complex with peptide MRTEPRPPAP of EMBOW Deposited 2024-11-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291.15 K；0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.72 Å R-free 0.210
9L0T Structure of WDR5 in complex with WIN motif containing RBM15 Deposited 2024-12-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M imidazole malate, pH 6.0, and 15 % (w/v) PEG 4000
Resolution 2.05 Å R-free 0.245
9L0T Structure of WDR5 in complex with WIN motif containing RBM15 Deposited 2024-12-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M imidazole malate, pH 6.0, and 15 % (w/v) PEG 4000
Resolution 2.05 Å R-free 0.245
9L0V Structure of WDR5 in complex with WIN motif containing ZSCAN10 Deposited 2024-12-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium citrate, pH 4.5, and 20 % (w/v) PEG 4000
Resolution 2.00 Å R-free 0.220
9LWY Crystal structure of human WDR5 in complex with compound 4 Deposited 2025-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded GOL GLYCEROL × 1 A1EMB 4-[[2-(6-fluoranyl-2-methyl-pyridin-3-yl)-6-(5-methyl-1,3-thiazol-2-yl)pyridin-4-yl]methyl]-1-methyl-imidazol-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, Bis-Tris, ammonium acetate
Resolution 1.55 Å R-free 0.191
9NCT Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded A1BW7 4-({6-cyclopropyl-8-[(2-methyl-1H-imidazol-1-yl)methyl]-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazol-3-yl}methyl)-2-methoxybenzonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；Ammonium Acetate, PEG 3350, Bis-TRS, TRIS, or HEPES
Resolution 2.11 Å R-free 0.228
9NCT Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded A1BW7 4-({6-cyclopropyl-8-[(2-methyl-1H-imidazol-1-yl)methyl]-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazol-3-yl}methyl)-2-methoxybenzonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；Ammonium Acetate, PEG 3350, Bis-TRS, TRIS, or HEPES
Resolution 2.11 Å R-free 0.228
9NCV Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded A1BW8 (6P)-6-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-3-[(4-fluoro-3-methylphenyl)methyl]-8-[(2-methyl-1H-imidazol-1-yl)methyl]-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG3350, Bis-TRIS, TRIS, HEPES
Resolution 1.58 Å R-free 0.287
9NCV Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded A1BW8 (6P)-6-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-3-[(4-fluoro-3-methylphenyl)methyl]-8-[(2-methyl-1H-imidazol-1-yl)methyl]-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG3350, Bis-TRIS, TRIS, HEPES
Resolution 1.58 Å R-free 0.287
9NCV Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 22–334（313 aa）
Not recorded A1BW8 (6P)-6-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-3-[(4-fluoro-3-methylphenyl)methyl]-8-[(2-methyl-1H-imidazol-1-yl)methyl]-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG3350, Bis-TRIS, TRIS, HEPES
Resolution 1.58 Å R-free 0.287
9NCV Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 22–334（313 aa）
Not recorded A1BW8 (6P)-6-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-3-[(4-fluoro-3-methylphenyl)methyl]-8-[(2-methyl-1H-imidazol-1-yl)methyl]-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG3350, Bis-TRIS, TRIS, HEPES
Resolution 1.58 Å R-free 0.287
9NCW Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded A1BW9 1-{[(6P)-3-[(3,5-dimethoxyphenyl)methyl]-6-(4-fluoro-2-methylphenyl)-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazol-8-yl]methyl}-3-methyl-1,3-dihydro-2H-imidazol-2-imine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG 3350, Bis-TRIS, HEPES, TRIS
Resolution 1.58 Å R-free 0.275
9NCW Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded A1BW9 1-{[(6P)-3-[(3,5-dimethoxyphenyl)methyl]-6-(4-fluoro-2-methylphenyl)-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazol-8-yl]methyl}-3-methyl-1,3-dihydro-2H-imidazol-2-imine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG 3350, Bis-TRIS, HEPES, TRIS
Resolution 1.58 Å R-free 0.275
9NCW Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG 3350, Bis-TRIS, HEPES, TRIS
Resolution 1.58 Å R-free 0.275
9NCW Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG 3350, Bis-TRIS, HEPES, TRIS
Resolution 1.58 Å R-free 0.275
9NSN Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41059 Deposited 2025-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded A1B0X N-{(1P)-5'-({(26E)-27-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-25-oxo-3,6,9,12,15,18,21-heptaoxa-24-azaheptacos-26-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-5,6-dihydropyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.15 M cesium chloride, 15% PEG3350
Resolution 1.85 Å R-free 0.234
9NSO Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41060 Deposited 2025-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded A1B0Y (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(34E)-1-{(1P)-6-fluoro-3'-[4-fluoro-2-(trifluoromethyl)benzamido]-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-1,33-dioxo-5,8,11,14,17,20,23,26,29-nonaoxa-2,32-diazapentatriacont-34-en-35-yl]-1H-pyrrole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.1 M sodium citrate tribasic dihydrate, pH 4.2, 0.4 M potassium phosphate dibasic, 1.6 M sodium phosphate monobasic monohydrate
Resolution 1.85 Å R-free 0.218
9UJR Crystal structure of WDR5 in complex with peptide Ac-MRT-NH2 Deposited 2025-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M HEPES pH 7.0, 30% v/v Jeffamine ED-2001 pH 7.0
Resolution 2.25 Å R-free 0.235
9UJZ Crystal structure of WDR5 in complex with peptide Ac-MRTEPRP-NH2 Deposited 2025-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M HEPES pH 7.0, 30% v/v Jeffamine ED-2001 pH 7.0
Resolution 2.46 Å R-free 0.229
9UK1 Crystal structure of WDR5 in complex with EMBOW Deposited 2025-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium tartrate dibasic dihydrate, 20% w/v Polyethylene glycol 3,350, pH7.3
Resolution 2.02 Å R-free 0.226
9UK3 Crystal structure of WDR5 in complex with peptide Ac-MRTEPRPPAP-NH2 Deposited 2025-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.69 Å R-free 0.200
9UK4 Crystal structure of WDR5 in complex with peptide Ac-ARA-NH2 Deposited 2025-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M HEPES pH 7.0, 30% v/v Jeffamine ED-2001 pH 7.0
Resolution 2.12 Å R-free 0.242
9UK7 Crystal structure of WDR5 in complex with peptide Ac-MRTEP-NH2 Deposited 2025-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000
Resolution 1.95 Å R-free 0.237
9UK7 Crystal structure of WDR5 in complex with peptide Ac-MRTEP-NH2 Deposited 2025-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000
Resolution 1.95 Å R-free 0.237
9UK7 Crystal structure of WDR5 in complex with peptide Ac-MRTEP-NH2 Deposited 2025-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000
Resolution 1.95 Å R-free 0.237
9UOJ WDR5 bound with P3 Deposited 2025-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–334（314 aa）
Not recorded A1L9J ~{N}-[5-[2-fluoranyl-5-[4-[[4-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-2,1,3-benzoxadiazol-7-yl]amino]butylcarbamoyl]phenyl]-2-[(3~{R},5~{S})-3,4,5-trimethylpiperazin-1-yl]phenyl]-6-oxidanylidene-4-(trifluoromethyl)-1~{H}-pyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；30% (w/v) polyethylene glycol 5000, 0.2 M ammonium sulfate, and 0.1 M MES monohydrate (pH 6.5)
Resolution 1.82 Å R-free 0.254
9UXG Structure of WDR5 in complex with Peptide 2 Deposited 2025-05-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium iodide, 0.1M Bis-tris propane pH 7.5, 20% w/v PEG 3350
Resolution 1.70 Å R-free 0.243
9UXJ Structure of WDR5 in complex with Peptide 2_R4A Deposited 2025-05-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M imidazole malate (pH 7.0), and 25 % w/v PEG 4000
Resolution 1.76 Å R-free 0.225
9UXM Structure of WDR5 in complex with Peptide 1 Deposited 2025-05-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium fluoride, 0.1 M Bis-Tris propane, pH 8.5, 20% w/v PEG3350
Resolution 1.48 Å R-free 0.193
9VN5 Structure of WDR5 in complex with MBD3C R43K Deposited 2025-06-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M imidazole malate (pH 8.5) and 7.5% w/v PEG 10,000
Resolution 1.90 Å R-free 0.231
9VN5 Structure of WDR5 in complex with MBD3C R43K Deposited 2025-06-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M imidazole malate (pH 8.5) and 7.5% w/v PEG 10,000
Resolution 1.90 Å R-free 0.231
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain R 1–334（334 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain R 1–334（334 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain R 1–334（334 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain R 1–334（334 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å

198 other PDB entries and 294 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name WDR5_HUMAN
Isoform —
PDB entities 10
Chains and sequence ranges Author chain R； PDBConstruct 1–334； UniProt 1–334

Protein dpy-30 homolog

Homo sapiens

UniProt Q9C005

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 15 DNA 2 PDB declaration: 17-meric（17） Consistent with all polymer counts Chain P； UniProt 1–99 Chain Q； UniProt 1–99 Not recorded Ubiquitin × 1 （P0CG47） [histone H3]-lysine(4) N-methyltransferase,Histone-lysine N-methyltransferase 2D × 1 （A0A6P6IDI8,O14686） Retinoblastoma-binding protein 5 × 1 （Q15291） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H3.1 × 2 （P68431） Histone H4 × 2 （P62805） Histone H2A type 1-B/E × 2 （P04908） Histone H2B type 2-E × 2 （Q16778） DNA (145-MER) × 1 WD repeat-containing protein 5 × 1 （P61964） DNA (145-MER) × 1 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.63 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9YLE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3G36 Crystal structure of the human DPY-30-like C-terminal domain Deposited 2009-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 45–99（55 aa） Fragment：C-terminal domain, UNI residues 45-99
Chain C 45–99（55 aa） Fragment：C-terminal domain, UNI residues 45-99
Mutation：L69M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L69M Non-standard monomer：Yes (specific site not provided by mmCIF) DTU (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 DTV (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.1M Bis-Tris, 28% PEG-MME 2000, 3% 1,6 hexanediol (additive), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.20 Å R-free 0.227
3G36 Crystal structure of the human DPY-30-like C-terminal domain Deposited 2009-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 45–99（55 aa） Fragment：C-terminal domain, UNI residues 45-99
Chain D 45–99（55 aa） Fragment：C-terminal domain, UNI residues 45-99
Mutation：L69M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L69M Non-standard monomer：Yes (specific site not provided by mmCIF) HEZ HEXANE-1,6-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.1M Bis-Tris, 28% PEG-MME 2000, 3% 1,6 hexanediol (additive), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.20 Å R-free 0.227
4RIQ Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30 Interacting region (SDI) Deposited 2014-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Chain B 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Chain D 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Chain E 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Chain J 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Chain K 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Chain V 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Chain Z 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；323 K；0.2M MgCl2, 25% PEG 3350, 0.1M Tris pH 8.5 and 10 mM spermidine, VAPOR DIFFUSION, SITTING DROP, temperature 323K
Resolution 2.23 Å R-free 0.284
4RIQ Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30 Interacting region (SDI) Deposited 2014-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Chain H 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Chain M 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Chain N 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Chain P 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Chain Q 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Chain S 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Chain T 45–99（55 aa） Fragment：UNP RESIDUES 45-99
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；323 K；0.2M MgCl2, 25% PEG 3350, 0.1M Tris pH 8.5 and 10 mM spermidine, VAPOR DIFFUSION, SITTING DROP, temperature 323K
Resolution 2.23 Å R-free 0.284
4RT4 Crystal structure of Dpy30 complexed with Bre2 Deposited 2014-11-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 41–99（59 aa） Fragment：C terminal domain, UNP residues 41-99
Chain B 41–99（59 aa） Fragment：C terminal domain, UNP residues 41-99
Chain C 41–99（59 aa） Fragment：C terminal domain, UNP residues 41-99
Chain D 41–99（59 aa） Fragment：C terminal domain, UNP residues 41-99
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.1M Tris-HCl, pH 8.5, 2.0M NH4H2PO4, EVAPORATION, temperature 291K
Resolution 2.00 Å R-free 0.224
4RTA Cystal structure of the Dpy30 for MLL/SET1 COMPASS H3K4 trimethylation Deposited 2014-11-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–99（99 aa）
Chain B 1–99（99 aa）
Not recorded FMT FORMIC ACID × 6 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.9；291 K；0.1M COCADYLATE SODIUM, SODIUM FORMATE 4.2M, pH 5.9, EVAPORATION, temperature 291K
Resolution 2.12 Å R-free 0.235
6E2H Crystal structure of human Ash2L (SPRY domain and SDI motif) in complex with full length DPY-30 Deposited 2018-07-11 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–99（99 aa）
Chain F 1–99（99 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20mM citrate pH 4.7 and polyethylene glycol (PEG) 6000
Resolution 2.24 Å R-free 0.200
6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain E 1–99（99 aa）
Chain F 1–99（99 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain P 1–99（99 aa）
Chain Q 1–99（99 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain P 1–99（99 aa）
Chain Q 1–99（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain P 1–99（99 aa）
Chain Q 1–99（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain P 1–99（99 aa）
Chain Q 1–99（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain P 1–99（99 aa）
Chain Q 1–99（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å

11 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPY30_HUMAN
Isoform —
PDB entities 12
Chains and sequence ranges Author chain P； PDBConstruct 1–99； UniProt 1–99 Author chain Q； PDBConstruct 1–99； UniProt 1–99

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9yle

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9yle
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9yle
Deposition date deposition_date2025-10-08
Structure title titleState 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac
Keywords keywordsMLL4 complex, histone modification, nucleosome recognition, transcription coactivation, TRANSCRIPTION, TRANSCRIPTION-DNA complex; TRANSCRIPTION/DNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier57.66 Å
Radius of gyration Rg (electron density) rg_electron57.85 Å
Forward intensity I(0) i02839350000.00
Molecular weight molecular_weight385160.0 kDa
Excluded volume excluded_volume456500 ų
Envelope volume envelope_volume775790 ų
Hydration-shell volume shell_volume112720 ų
Envelope diameter envelope_diameter210.2 Å
Shell Rg shell_rg61.49 Å
Envelope Rg envelope_rg56.33 Å
Shape Rg shape_rg57.85 Å
Total Rg total_rg57.95 Å
Total atoms total_atoms26696
Residues n_residues2908
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax195.4 Å
Rg (real space) rg_real57.60 Å
Rg uncertainty (real space) rg_real_error1.86 Å
I(0) (real space) i0_real2.8390e+09
I(0) uncertainty (real space) i0_real_error5.8340e+07
Rg (reciprocal space) rg_reciprocal57.70 Å
I(0) (reciprocal space) i0_reciprocal2840000000.0000
Solution quality estimate total_estimate0.8613
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary72.4 Å
Skewness Skewness skewness0.337
Kurtosis Kurtosis kurtosis-0.097
Angular range angular_range— – 0.1350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha192600000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.801; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.791
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (13)

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8. Citations (1)

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9. Files and Curves (10)