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4w5a

Complex structure of ATRX ADD bound to H3K9me3S10ph peptide

Method: X-RAY DIFFRACTION Dmax: 93.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Transcriptional regulator ATRX

Homo sapiens

UniProt P46100

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 167–289 Fragment：UNP residues 167-289 Mutation：K251R, F284Y Peptide from Histone H3.3 × 1 （P84243） ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2 Resolution 2.60 Å R-free 0.260
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 167–289 Fragment：UNP residues 167-289 Mutation：K251R, F284Y Peptide from Histone H3.3 × 1 （P84243） ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2 Resolution 2.60 Å R-free 0.260
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 167–289 Fragment：UNP residues 167-289 Mutation：K251R, F284Y Peptide from Histone H3.3 × 1 （P84243） ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2 Resolution 2.60 Å R-free 0.260

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 4W5A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2JM1 Structures and chemical shift assignments for the ADD domain of the ATRX protein Deposited 2006-09-13 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 159–296（138 aa） Fragment：ADD domain, residues 159-296
Not recorded ZN ZINC ION × 3 SOLUTION NMR
NMR measurement conditions pH 6.7；300 K；Ionic strength (raw mmCIF value) 0.5；Pressure ambient
NMR sample composition 0.7 mM [U-15N] ADD domain 156-296, 20 mM TRIS, 1 mM DTT, 100 uM zinc chloride, 0.5 M sodium chloride, 93% H2O, 7% D2O | 93% H2O/7% D2O
NMR sample composition 0.35 mM [U-13C; U-15N] ADD domain 156-296, 20 mM TRIS, 1 mM DTT, 100 uM zinc chloride, 0.5 M sodium chloride, 93% H2O, 7% D2O | 93% H2O/7% D2O
Resolution not provided
2LBM Solution structure of the ADD domain of ATRX complexed with histone tail H3 1-15 K9me3 Deposited 2011-04-08 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 159–296（138 aa） Fragment：UNP residues 159-296
Not recorded ZN ZINC ION × 3 SOLUTION NMR
NMR measurement conditions pH 7；300 K；Ionic strength (raw mmCIF value) 250；Pressure ambient
NMR sample composition 200 uM [U-98% 13C; U-98% 15N] ATRX ADD domain-1, 200 uM H3 tail 1-15 K9me3-2, 50 mM [U-99% 2H] TRIS-3, 200 mM sodium chloride-4, 150 uM zinc sulfate-5, 1 mM [U-99% 2H] DTT-6, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 200 uM [U-98% 13C; U-98% 15N] ATRX ADD domain-7, 200 uM H3 tail 1-15 K9me3-8, 50 mM [U-99% 2H] TRIS-9, 200 mM sodium chloride-10, 150 uM zinc sulfate-11, 1 mM [U-99% 2H] DTT-12, 100% D2O | 100% D2O
Resolution not provided
2LD1 Structures and chemical shift assignments for the ADD domain of the ATRX protein Deposited 2011-05-13 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 159–296（138 aa） Fragment：ADD DOMAIN, RESIDUES 159-296
Not recorded ZN ZINC ION × 3 SOLUTION NMR
NMR measurement conditions pH 6.7；300 K；Ionic strength (raw mmCIF value) 0.5；Pressure ambient
NMR sample composition 0.6-0.8 mM [U-15N] ADD_domain_163-296, 20 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 100 uM zinc chloride, 0.5 M sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.3-0.4 mM [U-13C; U-15N] ADD_domain_163-296, 20 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 100 uM zinc chloride, 0.5 M sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
3QL9 Monoclinic complex structure of ATRX ADD bound to histone H3K9me3 peptide Deposited 2011-02-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 167–289（123 aa） Fragment：N-terminal ADD domain, UNP residues 167-289
Mutation：K251R, F284Y ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；14% PEG 4000, 0.1M MES, 0.2 M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 0.93 Å R-free 0.131
3QLA Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide Deposited 2011-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 167–289（123 aa） Fragment：N-terminal ADD domain, UNP residues 167-289
Mutation：K251R, F284Y ZN ZINC ION × 3 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；14% PEG 4000, 0.1M MES, 0.2M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.60 Å R-free 0.179
3QLA Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide Deposited 2011-02-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 167–289（123 aa） Fragment：N-terminal ADD domain, UNP residues 167-289
Mutation：K251R, F284Y ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；14% PEG 4000, 0.1M MES, 0.2M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.60 Å R-free 0.179
3QLC Complex structure of ATRX ADD domain bound to unmodified H3 1-15 peptide Deposited 2011-02-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 167–289（123 aa） Fragment：N-terminal ADD domain, UNP residues 167-289
Mutation：K251R, F284Y ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；24% PEG 3350, 0.1M HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.50 Å R-free 0.241
3QLC Complex structure of ATRX ADD domain bound to unmodified H3 1-15 peptide Deposited 2011-02-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 167–289（123 aa） Fragment：N-terminal ADD domain, UNP residues 167-289
Mutation：K251R, F284Y ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；24% PEG 3350, 0.1M HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.50 Å R-free 0.241
3QLN Crystal structure of ATRX ADD domain in free state Deposited 2011-02-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 167–289（123 aa） Fragment：N-terminal ADD domain, UNP residues 167-289
Mutation：K251R, F284Y ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25% (v/v) PEG 4000, 100mM HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.90 Å R-free 0.158
3QLN Crystal structure of ATRX ADD domain in free state Deposited 2011-02-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 167–289（123 aa） Fragment：N-terminal ADD domain, UNP residues 167-289
Mutation：K251R, F284Y ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25% (v/v) PEG 4000, 100mM HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.90 Å R-free 0.158
5GRQ Crystal Structure of DHB domain of Daxx in complex with an ATRX peptide Deposited 2016-08-12 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 1256–1285（30 aa） Fragment：DID domain, UNP residues 1256-1285
Chain D 1256–1285（30 aa） Fragment：DID domain, UNP residues 1256-1285
Not recorded ACT ACETATE ION × 5 GOL GLYCEROL × 1 CL CHLORIDE ION × 4 ZN ZINC ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；100mM MES 6.0, 100mM zinc acetate, 13% ethanol
Resolution 1.58 Å R-free 0.179
5Y18 Crystal structure of DAXX helical bundle domain in complex with ATRX Deposited 2017-07-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1268–1289（22 aa） Fragment：UNP residues 1268-1289
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；289 K；0.1M sodium citrate, pH6.5, 0.2M ammonium acetate, 30% PEG4000
Resolution 2.20 Å R-free 0.219
5Y6O Crystal structure of DAXX N-terminal four-helix bundle domain (4HB) in complex with ATRX Deposited 2017-08-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288
Chain B 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288
Chain C 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；The DAXX 4HB_ATRX DBM fusion protein at 26 mg/ml was crystallized under conditions of 0.1M Sodium Cacodylate, pH 6.8, 1.2 M Ammonium Sulfate and 3% 1, 5- Diaminopentane Dihydrochloride, using sitting-drop vapor-diffusion method at 293K. In this process, o.5 uL of protein was mixed with 0.5 uL of mother liquor. All the crystals were soaked in a cryoprotectant made from mother liquor supplemented with 25% glycerol before flash freezing in liquid nitrogen.
Resolution 3.10 Å R-free 0.297
5Y6O Crystal structure of DAXX N-terminal four-helix bundle domain (4HB) in complex with ATRX Deposited 2017-08-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288
Chain E 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288
Chain F 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；The DAXX 4HB_ATRX DBM fusion protein at 26 mg/ml was crystallized under conditions of 0.1M Sodium Cacodylate, pH 6.8, 1.2 M Ammonium Sulfate and 3% 1, 5- Diaminopentane Dihydrochloride, using sitting-drop vapor-diffusion method at 293K. In this process, o.5 uL of protein was mixed with 0.5 uL of mother liquor. All the crystals were soaked in a cryoprotectant made from mother liquor supplemented with 25% glycerol before flash freezing in liquid nitrogen.
Resolution 3.10 Å R-free 0.297
5Y6O Crystal structure of DAXX N-terminal four-helix bundle domain (4HB) in complex with ATRX Deposited 2017-08-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric
Chain G 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288
Chain H 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288
Chain I 1265–1288（24 aa） Fragment：UNP residues 50-144,UNP residues 1265-1288
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；The DAXX 4HB_ATRX DBM fusion protein at 26 mg/ml was crystallized under conditions of 0.1M Sodium Cacodylate, pH 6.8, 1.2 M Ammonium Sulfate and 3% 1, 5- Diaminopentane Dihydrochloride, using sitting-drop vapor-diffusion method at 293K. In this process, o.5 uL of protein was mixed with 0.5 uL of mother liquor. All the crystals were soaked in a cryoprotectant made from mother liquor supplemented with 25% glycerol before flash freezing in liquid nitrogen.
Resolution 3.10 Å R-free 0.297
6G0O Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated ATRX peptide (K1030ac/K1033ac) Deposited 2018-03-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1027–1037（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；20.0 % PEG 6K 10.0 % EtGly 0.1 M HEPES pH 7.0 0.2 M LiCl
Resolution 1.40 Å R-free 0.166

11 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ATRX_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 7–129； UniProt 167–289 Author chain B； PDBConstruct 7–129； UniProt 167–289 Author chain E； PDBConstruct 7–129； UniProt 167–289

Peptide from Histone H3.3

OrganismNot specified

UniProt P84243

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 2–16 Non-standard monomer：Yes (specific site not provided by mmCIF) Transcriptional regulator ATRX × 1 （P46100） ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2 Resolution 2.60 Å R-free 0.260
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 2–16 Non-standard monomer：Yes (specific site not provided by mmCIF) Transcriptional regulator ATRX × 1 （P46100） ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2 Resolution 2.60 Å R-free 0.260
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain F； UniProt 2–16 Non-standard monomer：Yes (specific site not provided by mmCIF) Transcriptional regulator ATRX × 1 （P46100） ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2 Resolution 2.60 Å R-free 0.260

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 4W5A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2L43 Structural basis for histone code recognition by BRPF2-PHD1 finger Deposited 2010-10-01 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 2–13（12 aa）
Mutation：C29S, C36S ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.7；293 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient
NMR sample composition 0.8mM [U-100% 13C; U-100% 15N] protein-1, 1.6mM ZINC ION-2, 20mM Bis-Tris-3, 150mM sodium chloride-4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8mM [U-100% 13C; U-100% 15N] protein-5, 1.6mM ZINC ION-6, 20mM Bis-Tris-7, 150mM sodium chloride-8, 100% D2O | 100% D2O
Resolution not provided
3ASK Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 2–14（13 aa） Fragment：residues in UNP 2-14
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris propane, 200mM sodium citrate, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.90 Å R-free 0.286
3ASK Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Q 2–14（13 aa） Fragment：residues in UNP 2-14
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris propane, 200mM sodium citrate, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.90 Å R-free 0.286
3ASK Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 2–14（13 aa） Fragment：residues in UNP 2-14
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 6.5；277 K；0.1M Bis-Tris propane, 200mM sodium citrate, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.90 Å R-free 0.286
3ASL Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–12（11 aa） Fragment：residues in UNP 2-12
Not recorded ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10mM sodium citrate, 42% PEGMME2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.41 Å R-free 0.196
3AV2 The human nucleosome structure containing the histone variant H3.3 Deposited 2011-02-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 2.80 Å R-free 0.272
3JVK Crystal structure of bromodomain 1 of mouse Brd4 in complex with histone H3-K(ac)14 Deposited 2009-09-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 13–20（8 aa） Fragment：UNP residues 13-20
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；3.6M Na formate, 10% glycerol, soaked with 10-times excess of histone peptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.80 Å R-free 0.259
3MUK Crystal structure of Brd4 bromodomain 1 with propionylated histone H3-K(prop)23 Deposited 2010-05-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 22–29（8 aa） Fragment：histone H3 peptide, UNP residues 22-29
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；3.6M Na formate, 10% glycerol, soaked with 20-times excess of histone octapeptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.75 Å R-free 0.219
3MUL Crystal structure of Brd4 bromodomain 1 with butyrylated histone H3-K(buty)14 Deposited 2010-05-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 13–20（8 aa） Fragment：histone H3 peptide, UNP residues 13-20
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；3.6M Na formate, 10% glycerol, soaked with 20-times excess of histone octapeptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.65 Å R-free 0.226
3QL9 Monoclinic complex structure of ATRX ADD bound to histone H3K9me3 peptide Deposited 2011-02-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–16（15 aa） Fragment：K9 trimethylated H3 N-terminal fragment, UNP residues 2-16
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；14% PEG 4000, 0.1M MES, 0.2 M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 0.93 Å R-free 0.131
3QLA Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide Deposited 2011-02-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 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 × 3 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；14% PEG 4000, 0.1M MES, 0.2M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.60 Å R-free 0.179
3QLA Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide Deposited 2011-02-02 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 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 × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；14% PEG 4000, 0.1M MES, 0.2M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.60 Å R-free 0.179
3QLC Complex structure of ATRX ADD domain bound to unmodified H3 1-15 peptide Deposited 2011-02-02 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–16（15 aa） Fragment：N-terminal tail, UNP residues 2-16
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；24% PEG 3350, 0.1M HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.50 Å R-free 0.241
3QLC Complex structure of ATRX ADD domain bound to unmodified H3 1-15 peptide Deposited 2011-02-02 Different construct Different mutation/modification 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
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；24% PEG 3350, 0.1M HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.50 Å R-free 0.241
3WTP Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3 Deposited 2014-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
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 2.67 Å R-free 0.270
4GNE Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-7 Deposited 2012-08-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–8（7 aa） Fragment：UNP RESIDUES 2-8
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；283 K；0.1M Tris-HCl pH 7.0, 30% (w/v) PEG 3000, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 1.47 Å R-free 0.178
4GNF Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-15 Deposited 2012-08-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–16（15 aa） Fragment：UNP RESIDUES 2-16
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；0.1M Hepes pH 7.5, 70% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 1.55 Å R-free 0.205
4GNG Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide Deposited 2012-08-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–16（15 aa） Fragment：UNP RESIDUES 2-16
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；0.1M Mes pH 6.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 1.73 Å R-free 0.214
4GNG Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide Deposited 2012-08-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–16（15 aa） Fragment：UNP RESIDUES 2-16
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；0.1M Mes pH 6.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Resolution 1.73 Å R-free 0.214
4GU0 Crystal structure of LSD2 with H3 Deposited 2012-08-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 2–27（26 aa） Fragment：UNP residues 2-27
Mutation：K4M FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M (NH4)2 Tartrate, 0.1M HEPES, 10% PEG20000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.221
4GU0 Crystal structure of LSD2 with H3 Deposited 2012-08-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 2–27（26 aa） Fragment：UNP residues 2-27
Mutation：K4M FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M (NH4)2 Tartrate, 0.1M HEPES, 10% PEG20000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.221
4GUR Crystal structure of LSD2-NPAC with H3 in space group P21 Deposited 2012-08-29 Different construct Different mutation/modification 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 2–22（21 aa） Fragment：UNP residues 2-22
Mutation：K4M FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.51 Å R-free 0.204
4GUS Crystal structure of LSD2-NPAC with H3 in space group P3221 Deposited 2012-08-29 Different construct Different mutation/modification 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 2–22（21 aa） Fragment：UNP residues 2-22
Mutation：K4M FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 IOD IODIDE ION × 6 GOL GLYCEROL × 2 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；0.1M Ammonium Iodide, 0.1M MES, 10% PEG3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.23 Å R-free 0.237
4GY5 Crystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3 Deposited 2012-09-05 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2–18（17 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；20% PEG 3350, 200mM Ammonium Tartrate, 100mM Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.96 Å R-free 0.288
4GY5 Crystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3 Deposited 2012-09-05 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 2–18（17 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；20% PEG 3350, 200mM Ammonium Tartrate, 100mM Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.96 Å R-free 0.288
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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–136（135 aa）
Mutation：S96A, Y99F, G102A, A111T, M120F 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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–136（135 aa）
Mutation：G90M, S96A, Y99F, G102A, A111T, M120F 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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–136（135 aa）
Mutation：G90A, S96A, Y99F, G102A, A111T, M120F 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 conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–136（135 aa）
Mutation：G90A, S96A, Y99F, G102A, A111T, M120F 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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–136（135 aa）
Mutation：S96A, Y99F, G102A, A111T, M120F 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 conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–136（135 aa）
Mutation：S96A, Y99F, G102A, A111T, M120F 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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–136（135 aa）
Mutation：G90A, S96A, Y99F, G102A, A111T, M120F 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 conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–136（135 aa）
Mutation：G90A, S96A, Y99F, G102A, A111T, M120F 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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–136（135 aa）
Mutation：A75C, F84W, S96A, Y99F, G102A, A111T, M120F 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 conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–136（135 aa）
Mutation：A75C, F84W, S96A, Y99F, G102A, A111T, M120F 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–136（135 aa）
Chain B 2–136（135 aa）
Mutation：A75C, F84W, S96A, Y99F, G102A, A111T, M120F Mutation：A75C, F84W, S96A, Y99F, G102A, A111T, M120F 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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–136（136 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
4N4I Crystal structure of the Bromo-PWWP of the mouse zinc finger MYND-type containing 11 isoform alpha in complex with histone H3.3K36me3 Deposited 2013-10-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 20–43（24 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 2.00 Å R-free 0.245
4QQ4 CW-type zinc finger of MORC3 in complex with the amino terminus of histone H3 Deposited 2014-06-26 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 2–16（15 aa） Fragment：unp residues 2-16
Chain D 2–16（15 aa） Fragment：unp residues 2-16
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 UNX UNKNOWN LIGAND × 7 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG-3350, 0.2 M ammonium chloride, vapor diffusion, sitting drop, temperature 293K
Resolution 1.75 Å R-free 0.223
4TMP Crystal structure of AF9 YEATS bound to H3K9ac peptide Deposited 2014-06-02 Different construct Different ligand/ion 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 5.6；291 K；20% PEG4000, 5% 2-Propanol, 0.1 M Sodium Citrate Tribasic Dihydrate
Resolution 2.30 Å R-free 0.229
4TMP Crystal structure of AF9 YEATS bound to H3K9ac peptide Deposited 2014-06-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–12（11 aa） Fragment：UNP residues 2-12
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；20% PEG4000, 5% 2-Propanol, 0.1 M Sodium Citrate Tribasic Dihydrate
Resolution 2.30 Å R-free 0.229
4U7T Crystal structure of DNMT3A-DNMT3L in complex with histone H3 Deposited 2014-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 2–13（12 aa）
Chain G 2–13（12 aa）
Not recorded ZN ZINC ION × 6 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1M Sodium Acetate, 0.6M Ammonium Sulfate
Resolution 2.90 Å R-free 0.261
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 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 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 mutation/modification Different oligomeric state Different ligand/ion 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 2.92 Å R-free 0.252
5BNV Crystal structure of Human MCM2 HBD chaperoning a histone H3-H4 tetramer Deposited 2015-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 58–136（79 aa） Fragment：UNP residues 58-136
Chain D 58–136（79 aa） Fragment：UNP residues 58-136
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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 58–136（79 aa） Fragment：UNP residues 58-136
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
5DWQ Crystal structure of CARM1, sinefungin, and methylated H3 peptide (R17) Deposited 2015-09-22 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 F 14–31（18 aa） Fragment：UNP residues 14-31
Non-standard monomer：Yes (specific site not provided by mmCIF) SFG SINEFUNGIN × 2 GOL GLYCEROL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350
Resolution 2.36 Å R-free 0.257
5DWQ Crystal structure of CARM1, sinefungin, and methylated H3 peptide (R17) Deposited 2015-09-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 14–31（18 aa） Fragment：UNP residues 14-31
Non-standard monomer：Yes (specific site not provided by mmCIF) SFG SINEFUNGIN × 2 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350
Resolution 2.36 Å R-free 0.257
5DX0 Crystal structure of CARM1, sinefungin, and H3 peptide (R17) Deposited 2015-09-23 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 F 14–31（18 aa） Fragment：UNP residues 14-31
Chain G 14–31（18 aa） Fragment：UNP residues 14-31
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SFG SINEFUNGIN × 2 GOL GLYCEROL × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350
Resolution 2.05 Å R-free 0.263
5DX0 Crystal structure of CARM1, sinefungin, and H3 peptide (R17) Deposited 2015-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 14–31（18 aa） Fragment：UNP residues 14-31
Chain I 14–31（18 aa） Fragment：UNP residues 14-31
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) SFG SINEFUNGIN × 2 GOL GLYCEROL × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350
Resolution 2.05 Å R-free 0.263
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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 58–136（79 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
5JJY Crystal structure of SETD2 bound to histone H3.3 K36M peptide Deposited 2016-04-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 30–43（14 aa） Fragment：H3 peptide, UNP residues 30-43
Mutation：K36M ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SCN THIOCYANATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2 M KSCN, 0.1 M Bis-Tris Propane, 20% PEG3350
Resolution 2.05 Å R-free 0.213
5JLB Crystal structure of SETD2 bound to histone H3.3 K36I peptide Deposited 2016-04-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 30–43（14 aa） Fragment：H3 peptide, UNP residues 30-43
Mutation：K36I SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SCN THIOCYANATE ION × 3 GOL GLYCEROL × 2 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2 M KSCN, 0.1 M Bis-Tris Propane, 20% PEG3350
Resolution 1.50 Å R-free 0.190
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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–136（135 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 mutation/modification Different oligomeric state Different ligand/ion 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
Resolution 2.18 Å R-free 0.256
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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
6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 4–18（15 aa）
Mutation：K9R ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
Resolution 2.33 Å R-free 0.280
6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 4–18（15 aa）
Mutation：K9R ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
Resolution 2.33 Å R-free 0.280
6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 4–18（15 aa）
Mutation：K9R ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
Resolution 2.33 Å R-free 0.280
6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 4–18（15 aa）
Mutation：K9R ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
Resolution 2.33 Å R-free 0.280
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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
6PZV Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin Deposited 2019-08-01 Different construct 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 2–27（26 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；277 K；0.1M citric acid (pH 3.5), 28% PEG8000
Resolution 3.01 Å R-free 0.272
6PZV Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin Deposited 2019-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 2–27（26 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 3.5；277 K；0.1M citric acid (pH 3.5), 28% PEG8000
Resolution 3.01 Å R-free 0.272
6R0C Human-D02 Nucleosome Core Particle with biotin-streptavidin label Deposited 2019-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–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 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6RNY PFV intasome - nucleosome strand transfer complex Deposited 2019-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: octadecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 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
6U04 Crystal structure of human BRPF1 PZP bound to histone H3 tail Deposited 2019-08-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–13（12 aa）
Not recorded PR PRASEODYMIUM ION × 1 ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；0.2 M Lithium sulfate, 0.1 M Tris-HCl pH 8.5, 40% (v/v) PEG400, and 0.01M Praseodymium(III) acetate hydrate
Resolution 2.20 Å R-free 0.208
7A08 CryoEM Structure of cGAS Nucleosome complex Deposited 2020-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain d 2–136（135 aa）
Chain h 2–136（135 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
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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 58–136（79 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 58–136（79 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 58–136（79 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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 58–136（79 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 58–136（79 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
7CWH Structural basis of RACK7 PHD to read a pediatric glioblastoma-associated histone mutation H3.3G34R Deposited 2020-08-28 Different construct Different mutation/modification 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 32–42（11 aa）
Mutation：G34R ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.4；293 K；Ionic strength (raw mmCIF value) 500；Pressure 1
NMR sample composition 0.7 mM [U-13C; U-15N] RACK7 PHD, 1.4 mM H3.3G34R, 100 mM sodium chloride, 0.02 % w/v sodium azide, 50 mM sodium phosphate, 2 mM [U-2H] DDT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.7 mM [U-13C; U-15N] RACK7 PHD, 1.4 mM H3.3G34R, 100 mM sodium chloride, 0.02 % w/v sodium azide, 50 mM sodium phosphate, 2 mM [U-2H] DTT, 100% D2O | 100% D2O
NMR sample composition 1 mM [U-13C; U-15N] G34R, 1.2 mM RACK7 PHD, 100 mM sodium chloride, 0.02 % w/v sodium azide, 50 mM sodium phosphate, 2 mM [U-2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7OKP Crystal structure of mouse CARM1 in complex with histone H3_13-22 K18 acetylated Deposited 2021-05-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 14–23（10 aa）
Chain F 14–23（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MLI MALONATE ION × 2 QVR (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1M sodium malonate, 0.1M MES pH7.0, 0.2M sodium chloride
Resolution 2.20 Å R-free 0.254
7OKP Crystal structure of mouse CARM1 in complex with histone H3_13-22 K18 acetylated Deposited 2021-05-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 14–23（10 aa）
Chain H 14–23（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MLI MALONATE ION × 8 QVR (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1M sodium malonate, 0.1M MES pH7.0, 0.2M sodium chloride
Resolution 2.20 Å R-free 0.254
7V1L Structure of sNASP core in complex with H3 alpha3 helix peptide Deposited 2021-08-04 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 V 117–136（20 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.4M Na-K phosphate, pH 8.2
Resolution 2.85 Å R-free 0.246
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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–136（135 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–136（135 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
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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 58–136（79 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 58–136（79 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 58–136（79 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
7W5M Crystal structure of AtNASP in complex of H3 alpha3 helix peptide Deposited 2021-11-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 117–136（20 aa）
Not recorded GOL GLYCEROL × 1 PG4 TETRAETHYLENE GLYCOL × 2 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20% PEG 300, 0.2M Ammonium sulfate, 0.1M Phosphate citrate, pH 4.2, 10% Glycerol
Resolution 2.15 Å R-free 0.227
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 e 1–136（136 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
9B3P The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome Deposited 2024-03-19 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）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Tris-HCl, 5mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE；Freezing condition: blot force 0, blot time 4.5 second
Resolution 3.00 Å
9EOZ Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0 Deposited 2024-03-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain E 2–136（135 aa）
Chain K 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 3.10 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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
9J0N Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc) Deposited 2024-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 27 PDB declaration: 30-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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
9L1X hDEK-nucleosome complex (conformation 1) Deposited 2024-12-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 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 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 × 10 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 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
9UTH DPF3b in complex with H3K14cr peptide Deposited 2025-05-03 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 B 2–27（26 aa）
Chain D 2–27（26 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, SITTING DROP；277.15 K；4 M Sodium Formate, pH 7.0
Resolution 2.69 Å R-free 0.230
9UTH DPF3b in complex with H3K14cr peptide Deposited 2025-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 2–27（26 aa）
Chain H 2–27（26 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, SITTING DROP；277.15 K；4 M Sodium Formate, pH 7.0
Resolution 2.69 Å R-free 0.230
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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Mutation：K36M Mutation：K36M 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Mutation：K36M Mutation：K36M 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Mutation：K36M Mutation：K36M 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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 method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 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

94 other PDB entries and 121 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H33_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–15； UniProt 2–16 Author chain D； PDBConstruct 1–15； UniProt 2–16 Author chain F； PDBConstruct 1–15； UniProt 2–16

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 4w5a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4w5a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4w5a
Deposition date deposition_date2014-08-17
Structure title titleComplex structure of ATRX ADD bound to H3K9me3S10ph peptide
Keywords keywordsEpigenetic regulation, Complex, Transcription, Mitosis, HYDROLASE-STRUCTURAL PROTEIN complex; HYDROLASE/STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.25 Å
Radius of gyration Rg (electron density) rg_electron27.87 Å
Forward intensity I(0) i043862900.00
Molecular weight molecular_weight46837.0 kDa
Excluded volume excluded_volume56615 ų
Envelope volume envelope_volume74882 ų
Hydration-shell volume shell_volume24396 ų
Envelope diameter envelope_diameter94.2 Å
Shell Rg shell_rg32.91 Å
Envelope Rg envelope_rg27.67 Å
Shape Rg shape_rg27.90 Å
Total Rg total_rg28.28 Å
Total atoms total_atoms3210
Residues n_residues396
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 dmax93.8 Å
Rg (real space) rg_real28.56 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real4.3860e+07
I(0) uncertainty (real space) i0_real_error6.9760e+05
Rg (reciprocal space) rg_reciprocal28.47 Å
I(0) (reciprocal space) i0_reciprocal43860000.0000
Solution quality estimate total_estimate0.8359
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary25.1 Å
Skewness Skewness skewness0.504
Kurtosis Kurtosis kurtosis-0.491
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha8023000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.707; Smooth: 0.794
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)