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6w5i

Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class01)

Method: ELECTRON MICROSCOPY Dmax: 153.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Retinoblastoma-binding protein 5

Homo sapiens

UniProt Q15291

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 12 DNA 2 PDB declaration: tetradecameric（14） Consistent with all polymer counts Chain A； UniProt 2–538 Not recorded WD repeat-containing protein 5 × 1 （P61964） Histone-lysine N-methyltransferase 2A × 1 （Q03164） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A × 2 （Q6AZJ8） Histone H2B 1.1 × 2 （P02281） DNA (147-MER) × 1 DNA (147-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.90 Å

Other States of the Same Protein in the Database

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

Other PDB Difference from Current Entry 6W5I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3P4F Structural and biochemical insights into MLL1 core complex assembly and regulation. Deposited 2010-10-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 371–381（11 aa） Fragment：unp residues 371-381
Mutation：Y381D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；0.2 M ammonium citrate (buffered with hydrochloric acid/sodium hydroxide to pH 7.0) and 18% PEG3350, VAPOR DIFFUSION, HANGING DROP
Resolution 2.35 Å R-free 0.249
4X8N Crystal structure of Ash2L SPRY domain in complex with phosphorylated RbBP5 Deposited 2014-12-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 347–356（10 aa） Fragment：UNP residues 347-356
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol
Resolution 2.10 Å R-free 0.277
4X8P Crystal structure of Ash2L SPRY domain in complex with RbBP5 Deposited 2014-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 344–355（12 aa） Fragment：UNP residues 344-355
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol
Resolution 2.20 Å R-free 0.271
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 330–356（27 aa） Fragment：UNP RESIDUES 330-356
Chain F 330–356（27 aa） Fragment：UNP RESIDUES 330-356
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 330–356（27 aa） Fragment：UNP RESIDUES 330-356
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 330–356（27 aa） Fragment：UNP RESIDUES 330-356
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6L The crystal structure of MLL1 (N3861I/Q3867L) in complex with RbBP5 and Ash2L Deposited 2015-12-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 330–356（27 aa） Fragment：UNP RESIDUES 330-356
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；277 K；200mM NaCl, 20% PEG 3350
Resolution 1.90 Å R-free 0.213
6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain N 1–538（538 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain N 1–538（538 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIW Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain N 1–538（538 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIX Cryo-EM structure of human MLL1-NCP complex, binding mode1 Deposited 2019-07-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain N 1–538（538 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6KIZ Cryo-EM structure of human MLL1-NCP complex, binding mode2 Deposited 2019-07-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain N 1–538（538 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6KM7 The structural basis for the internal interaction in RBBP5 Deposited 2019-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 10–325（316 aa）
Chain C 390–480（91 aa） Fragment：C-terminal distal domain
Not recorded SO4 SULFATE ION × 2 2PE NONAETHYLENE GLYCOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.1 M HEPES-Na, pH 7.5, 2% w/v PEG 400, 2.0 M ammonium sulfate
Resolution 1.80 Å R-free 0.194
6KM7 The structural basis for the internal interaction in RBBP5 Deposited 2019-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 10–325（316 aa）
Chain D 390–480（91 aa） Fragment：C-terminal distal domain
Not recorded SO4 SULFATE ION × 6 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；0.1 M HEPES-Na, pH 7.5, 2% w/v PEG 400, 2.0 M ammonium sulfate
Resolution 1.80 Å R-free 0.194
6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain A 2–538（537 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
6PWW Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 2–538（537 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6PWX Cryo-EM structure of RbBP5 bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6W5N Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Deposited 2020-03-13 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7BRE The crystal structure of MLL2 in complex with ASH2L and RBBP5 Deposited 2020-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 330–356（27 aa）
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Ammonium tartrate dibasic pH 7.0, 12%(w/v) Polyethylene glycol 3,350
Resolution 2.80 Å R-free 0.265
7BRE The crystal structure of MLL2 in complex with ASH2L and RBBP5 Deposited 2020-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 330–356（27 aa）
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Ammonium tartrate dibasic pH 7.0, 12%(w/v) Polyethylene glycol 3,350
Resolution 2.80 Å R-free 0.265
7MBM Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Deposited 2021-04-01 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.76 Å
7MBN Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Deposited 2021-04-01 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–538（537 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain N 1–538（538 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
7W67 The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 330–356（27 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.19 Å R-free 0.222
7W6A Crystal structure of the MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L complex Deposited 2021-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 330–356（27 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5 25% w/v polyethylene glycol 3350
Resolution 2.21 Å R-free 0.229
7W6I The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me1 peptide Deposited 2021-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 330–356（27 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3,350
Resolution 2.56 Å R-free 0.244
7W6J The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me2 peptide Deposited 2021-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 330–356（27 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.68 Å R-free 0.252
7W6L The crystal structure of MLL3-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 330–356（27 aa）
Chain F 330–356（27 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM sodium cacodylate, pH 6.5, 10% polyethylene glycol 3350, 0.1 M MgCl2
Resolution 2.26 Å R-free 0.223
8DU4 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Deposited 2022-07-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLE State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.63 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain N 1–538（538 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å

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

View Construct and Data Evidence
UniProt name RBBP5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–538； UniProt 2–538

WD repeat-containing protein 5

Homo sapiens

UniProt P61964

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 12 DNA 2 PDB declaration: tetradecameric（14） Consistent with all polymer counts Chain B； UniProt 22–334 Not recorded Retinoblastoma-binding protein 5 × 1 （Q15291） Histone-lysine N-methyltransferase 2A × 1 （Q03164） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A × 2 （Q6AZJ8） Histone H2B 1.1 × 2 （P02281） DNA (147-MER) × 1 DNA (147-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.90 Å

Other States of the Same Protein in the Database

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

Other PDB Difference from Current Entry 6W5I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10TC Structure of WDR5 bound to RbBP5 (D376N) Deposited 2026-02-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 31–334（304 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.15 M Ammonium citrate, 18% PEG3350
Resolution 2.20 Å R-free 0.243
10TC Structure of WDR5 bound to RbBP5 (D376N) Deposited 2026-02-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 31–334（304 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.15 M Ammonium citrate, 18% PEG3350
Resolution 2.20 Å R-free 0.243
10TC Structure of WDR5 bound to RbBP5 (D376N) Deposited 2026-02-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 31–334（304 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.15 M Ammonium citrate, 18% PEG3350
Resolution 2.20 Å R-free 0.243
10TC Structure of WDR5 bound to RbBP5 (D376N) Deposited 2026-02-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 31–334（304 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.15 M Ammonium citrate, 18% PEG3350
Resolution 2.20 Å R-free 0.243
24XN Structure of WDR5 F263A variant in complex with MBD3C Deposited 2026-03-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.15 ammonium sulfate, 0.1 M sodium HEPES, pH7.0, 20% w/v PEG 4000
Resolution 1.57 Å R-free 0.212
24XN Structure of WDR5 F263A variant in complex with MBD3C Deposited 2026-03-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.15 ammonium sulfate, 0.1 M sodium HEPES, pH7.0, 20% w/v PEG 4000
Resolution 1.57 Å R-free 0.212
24XP Crystal structure of WDR5 F133A variant in complex with MBD3C Deposited 2026-03-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M sodium acetate (pH 5.0), 20% (w/v) PEG 4000
Resolution 1.30 Å R-free 0.180
24XP Crystal structure of WDR5 F133A variant in complex with MBD3C Deposited 2026-03-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M sodium acetate (pH 5.0), 20% (w/v) PEG 4000
Resolution 1.30 Å R-free 0.180
2CNX WDR5 and Histone H3 Lysine 4 dimethyl complex at 2.1 angstrom Deposited 2006-05-25 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 20–334（315 aa） Fragment：RESIDUES 20-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.223
2CO0 WDR5 and unmodified Histone H3 complex at 2.25 Angstrom Deposited 2006-05-25 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 20–334（315 aa） Fragment：RESIDUES 20-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.25 Å R-free 0.226
2CO0 WDR5 and unmodified Histone H3 complex at 2.25 Angstrom Deposited 2006-05-25 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 20–334（315 aa） Fragment：RESIDUES 20-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.25 Å R-free 0.226
2G99 Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5 Deposited 2006-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 27–334（308 aa） Fragment：residues 27-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG 4000, 10% isopropanol, 0.1M HEPES, pH7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.90 Å R-free 0.243
2G99 Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5 Deposited 2006-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 27–334（308 aa） Fragment：residues 27-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG 4000, 10% isopropanol, 0.1M HEPES, pH7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.90 Å R-free 0.243
2G9A Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5 Deposited 2006-03-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 29–334（306 aa） Fragment：;'residues 24-334 ;
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG, 0.2M ammonium acetate, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.70 Å R-free 0.286
2GNQ Structure of wdr5 Deposited 2006-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–334（334 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；20%peg5k mme, bis-tris 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Resolution 1.80 Å R-free 0.192
2H13 Crystal structure of WDR5/histone H3 complex Deposited 2006-05-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa） Fragment：Residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；20-30% PEG3350, 0.1 M HEPES, pH 7.5, 0.05 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP
Resolution 1.58 Å R-free 0.200
2H14 Crystal of WDR5 (apo-form) Deposited 2006-05-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa） Fragment：Residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；20-30% PEG 3350 0.1M Hepes 0.05M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP
Resolution 1.48 Å R-free 0.197
2H68 Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-05-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.79 Å R-free 0.192
2H68 Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-05-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.79 Å R-free 0.192
2H6K Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-05-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris, HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.89 Å R-free 0.190
2H6K Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-05-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris, HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.89 Å R-free 0.190
2H6N Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-05-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.50 Å R-free 0.198
2H6N Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-05-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.50 Å R-free 0.198
2H6Q Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-06-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.87 Å R-free 0.185
2H6Q Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex Deposited 2006-06-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa） Fragment：residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Crystals were grown by hanging drop vapour equilibration in Nextal plates as follows: 1 ul of 10 15 mg ml-1 protein solution (10 mM Tris HCl (pH 7.4), 50 mM NaCl, and 10 mM 2-mercaptoethanol) were mixed with 1 ul of well solution composed of 50 mM HEPES (pH 7.5), 100 mM potassium formate, and 10-20% (w/v) polyethylene glycol 3350 and equilibrated at room temperature overnight against 1 ml of well solution.
Resolution 1.87 Å R-free 0.185
2H9L WDR5delta23 Deposited 2006-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；20% PEG 5000 MME, 0.1M Bis-Tris 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Resolution 1.75 Å R-free 0.201
2H9M WDR5 in complex with unmodified H3K4 peptide Deposited 2006-06-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；20% PEG 3350, 0.2M di-Na Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.90 Å R-free 0.257
2H9M WDR5 in complex with unmodified H3K4 peptide Deposited 2006-06-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；300 K；20% PEG 3350, 0.2M di-Na Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.90 Å R-free 0.257
2H9N WDR5 in complex with monomethylated H3K4 peptide Deposited 2006-06-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.00 Å R-free 0.279
2H9N WDR5 in complex with monomethylated H3K4 peptide Deposited 2006-06-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.00 Å R-free 0.279
2H9P WDR5 in complex with trimethylated H3K4 peptide Deposited 2006-06-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；300 K；30% PEG4000, 0.2M Ammonium Acetate and 0.1M Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.91 Å R-free 0.203
2O9K WDR5 in Complex with Dimethylated H3K4 Peptide Deposited 2006-12-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；20% PEG 5000 MME, 0.1M BIS-TRIS, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K, pH 6.50
Resolution 1.90 Å R-free 0.226
2O9K WDR5 in Complex with Dimethylated H3K4 Peptide Deposited 2006-12-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；20% PEG 5000 MME, 0.1M BIS-TRIS, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K, pH 6.50
Resolution 1.90 Å R-free 0.226
3EG6 Structure of WDR5 bound to MLL1 peptide Deposited 2008-09-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：WD-repeat domain (UNP residues 23-334)
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；298 K；30% PEG 3350, 30 mM (NH4)2SO4, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.72 Å R-free 0.240
3EMH Structural basis of WDR5-MLL interaction Deposited 2008-09-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 25–334（310 aa） Fragment：UNP residues 25-334
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20 mM HEPES, 15-20% PEG 3350, 60mM Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.37 Å R-free 0.200
3MXX Crystal structure of WDR5 mutant (S62A) Deposited 2010-05-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa） Fragment：RESIDUES 31-334
Mutation：S62A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；18% PEG 3350, 0.1M Hepes, 18mM (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.05 Å R-free 0.239
3N0D Crystal structure of WDR5 mutant (W330F) Deposited 2010-05-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa） Fragment：RESIDUES 31-334
Mutation：W330F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；18% PEG 3350, 0.1M Hepes, 14mM (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.233
3N0E Crystal structure of WDR5 mutant (W330Y) Deposited 2010-05-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa） Fragment：RESIDUES 31-334
Mutation：W330Y No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；18% PEG 3350, 0.1M Hepes, 14mM (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.323
3P4F Structural and biochemical insights into MLL1 core complex assembly and regulation. Deposited 2010-10-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 22–334（313 aa） Fragment：unp residues 1-308
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；0.2 M ammonium citrate (buffered with hydrochloric acid/sodium hydroxide to pH 7.0) and 18% PEG3350, VAPOR DIFFUSION, HANGING DROP
Resolution 2.35 Å R-free 0.249
3PSL Fine-tuning the stimulation of MLL1 methyltransferase activity by a histone H3 based peptide mimetic Deposited 2010-12-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa） Fragment：WDR5 (unp residues 21-334)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；50 mM NaAcetate, 100 mM NH4 SO4 , and 20% PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.205
3PSL Fine-tuning the stimulation of MLL1 methyltransferase activity by a histone H3 based peptide mimetic Deposited 2010-12-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 21–334（314 aa） Fragment：WDR5 (unp residues 21-334)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；50 mM NaAcetate, 100 mM NH4 SO4 , and 20% PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.70 Å R-free 0.205
3SMR Crystal structure of human WD repeat domain 5 with compound Deposited 2011-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded NP7 2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 8 UNX UNKNOWN LIGAND × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；24% PEG3350,9.2M NH4 Acetate, 0.1 Bis Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 1.82 Å R-free 0.206
3SMR Crystal structure of human WD repeat domain 5 with compound Deposited 2011-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa）
Not recorded NP7 2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 6 UNX UNKNOWN LIGAND × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；24% PEG3350,9.2M NH4 Acetate, 0.1 Bis Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 1.82 Å R-free 0.206
3SMR Crystal structure of human WD repeat domain 5 with compound Deposited 2011-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 24–334（311 aa）
Not recorded NP7 2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 5 UNX UNKNOWN LIGAND × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；24% PEG3350,9.2M NH4 Acetate, 0.1 Bis Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 1.82 Å R-free 0.206
3SMR Crystal structure of human WD repeat domain 5 with compound Deposited 2011-06-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 24–334（311 aa）
Not recorded NP7 2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 4 UNX UNKNOWN LIGAND × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；24% PEG3350,9.2M NH4 Acetate, 0.1 Bis Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 1.82 Å R-free 0.206
3UR4 Crystal structure of human WD repeat domain 5 with compound Deposited 2011-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded 0BW methyl 3-[(3-methoxybenzoyl)amino]-4-(4-methylpiperazin-1-yl)benzoate × 1 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 4 SO4 SULFATE ION × 2 UNX UNKNOWN LIGAND × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；297 K；22% PEG 3350,0.1M A.S. ,0.1M Bis Tris pH 6.0 , VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 1.80 Å R-free 0.213
3UR4 Crystal structure of human WD repeat domain 5 with compound Deposited 2011-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa）
Not recorded 0BW methyl 3-[(3-methoxybenzoyl)amino]-4-(4-methylpiperazin-1-yl)benzoate × 1 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 2 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；297 K；22% PEG 3350,0.1M A.S. ,0.1M Bis Tris pH 6.0 , VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 1.80 Å R-free 0.213
3UVK Crystal structure of WDR5 in complex with the WDR5-interacting motif of MLL2 Deposited 2011-11-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa） Fragment：UNP residues 21-334
Not recorded BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；323 K；0.1 M ammonium sulfate, 24% PEG3350, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 323K
Resolution 1.40 Å R-free 0.192
3UVL Crystal structure of WDR5 in complex with the WDR5-interacting motif of MLL3 Deposited 2011-11-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa） Fragment：UNP residues 21-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；323 K；0.1 M ammonium acetate, 25% PEG3350, 0.1 M Bis-Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 323K
Resolution 2.20 Å R-free 0.220
3UVM Crystal structure of WDR5 in complex with the WDR5-interacting motif of MLL4 Deposited 2011-11-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa） Fragment：UNP residues 21-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.1 M ammonium sulfate, 25% PEG3350, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.57 Å R-free 0.198
3UVN Crystal structure of WDR5 in complex with the WDR5-interacting motif of SET1A Deposited 2011-11-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa） Fragment：UNP residues 21-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；25% PEG3350, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.79 Å R-free 0.230
3UVN Crystal structure of WDR5 in complex with the WDR5-interacting motif of SET1A Deposited 2011-11-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 21–334（314 aa） Fragment：UNP residues 21-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；25% PEG3350, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.79 Å R-free 0.230
3UVO Crystal structure of WDR5 in complex with the WDR5-interacting motif of SET1B Deposited 2011-11-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa） Fragment：UNP residues 21-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.1 M ammonium sulfate, 25% PEG3350, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.219
4A7J Symmetric Dimethylation of H3 Arginine 2 is a Novel Histone Mark that Supports Euchromatin Maintenance Deposited 2011-11-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa） Fragment：RESIDUES 21-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1 M HEPES PH 7.5; 60 MM AMMONIUM SULPHATE; 30% PEG 3350
Resolution 1.90 Å R-free 0.222
4CY1 Crystal structure of the KANSL1-WDR5 complex. Deposited 2014-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：RESIDUES 23-334
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；26% (W/V) PEG 3350, 0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS, PH 6.5.
Resolution 1.50 Å R-free 0.183
4CY1 Crystal structure of the KANSL1-WDR5 complex. Deposited 2014-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa） Fragment：RESIDUES 23-334
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；26% (W/V) PEG 3350, 0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS, PH 6.5.
Resolution 1.50 Å R-free 0.183
4CY2 Crystal structure of the KANSL1-WDR5-KANSL2 complex. Deposited 2014-04-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 23–334（312 aa） Fragment：RESIDUES 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.9；20% (W/V) PEG 3350, 0.2 M POTASSIUM NITRATE, PH 6.9.
Resolution 2.00 Å R-free 0.222
4ERQ X-ray structure of WDR5-MLL2 Win motif peptide binary complex Deposited 2012-04-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.3；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.3, hanging drop, temperature 294K
Resolution 1.91 Å R-free 0.200
4ERQ X-ray structure of WDR5-MLL2 Win motif peptide binary complex Deposited 2012-04-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.3；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.3, hanging drop, temperature 294K
Resolution 1.91 Å R-free 0.200
4ERQ X-ray structure of WDR5-MLL2 Win motif peptide binary complex Deposited 2012-04-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.3；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.3, hanging drop, temperature 294K
Resolution 1.91 Å R-free 0.200
4ERY X-ray structure of WDR5-MLL3 Win motif peptide binary complex Deposited 2012-04-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.5；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.5, hanging drop, temperature 294K
Resolution 1.30 Å R-free 0.209
4ERZ X-ray structure of WDR5-MLL4 Win motif peptide binary complex Deposited 2012-04-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.6；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.6, hanging drop, temperature 294K
Resolution 1.75 Å R-free 0.216
4ERZ X-ray structure of WDR5-MLL4 Win motif peptide binary complex Deposited 2012-04-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.6；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.6, hanging drop, temperature 294K
Resolution 1.75 Å R-free 0.216
4ERZ X-ray structure of WDR5-MLL4 Win motif peptide binary complex Deposited 2012-04-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.6；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.6, hanging drop, temperature 294K
Resolution 1.75 Å R-free 0.216
4ES0 X-ray structure of WDR5-SETd1b Win motif peptide binary complex Deposited 2012-04-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.6；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.6, hanging drop, temperature 294K
Resolution 1.82 Å R-free 0.242
4ESG X-ray structure of WDR5-MLL1 Win motif peptide binary complex Deposited 2012-04-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.2；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.2, hanging drop, temperature 294K
Resolution 1.70 Å R-free 0.193
4ESG X-ray structure of WDR5-MLL1 Win motif peptide binary complex Deposited 2012-04-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.2；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.2, hanging drop, temperature 294K
Resolution 1.70 Å R-free 0.193
4EWR X-ray structure of WDR5-SETd1a Win motif peptide binary complex Deposited 2012-04-27 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa） Fragment：UNP residues 23-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.6；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.6, hanging drop, temperature 294K
Resolution 1.50 Å R-free 0.198
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM3 Crystal structure of human WD repeat domain 5 with compound MM-101 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；25% PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.39 Å R-free 0.226
4GM8 Crystal structure of human WD repeat domain 5 with compound MM-102 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；30% PEG8000, 0.2 M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.249
4GM8 Crystal structure of human WD repeat domain 5 with compound MM-102 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；30% PEG8000, 0.2 M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.249
4GM8 Crystal structure of human WD repeat domain 5 with compound MM-102 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；30% PEG8000, 0.2 M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.249
4GM8 Crystal structure of human WD repeat domain 5 with compound MM-102 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；30% PEG8000, 0.2 M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.60 Å R-free 0.249
4GM9 Crystal structure of human WD repeat domain 5 with compound MM-401 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；30% PEG4000, 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Resolution 2.10 Å R-free 0.208
4GM9 Crystal structure of human WD repeat domain 5 with compound MM-401 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；30% PEG4000, 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Resolution 2.10 Å R-free 0.208
4GMB Crystal structure of human WD repeat domain 5 with compound MM-402 Deposited 2012-08-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa） Fragment：UNP residues 22-334
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% tert-butanol, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.78 Å R-free 0.247
4IA9 Crystal structure of human WD REPEAT DOMAIN 5 in complex with 2-chloro-4-fluoro-3-methyl-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide Deposited 2012-12-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded IA9 2-chloro-4-fluoro-3-methyl-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 2 UNX UNKNOWN LIGAND × 24 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；291 K；25% PEH 3500, 0.1 M Ammonium sulfate, 0.1 M BisTris pH5.5, vapor diffusion hanging drop, temperature 291K
Resolution 1.66 Å R-free 0.210
4O45 WDR5 in complex with influenza NS1 C-terminal tail Deposited 2013-12-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa） Fragment：UNP residues 24-334
Not recorded UNX UNKNOWN LIGAND × 17 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；291 K；25% PEG3350, 0.1 M ammonium sulfate, 0.1 M bis-tris, pH 6.5, temperature 291K
Resolution 1.87 Å R-free 0.212
4QL1 Crystal structure of human WDR5 in complex with compound OICR-9429 Deposited 2014-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded 35Q N-(4-(4-methylpiperazin-1-yl)-3'-(morpholinomethyl)-[1,1'-biphenyl]-3-yl)-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 UNX UNKNOWN LIGAND × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；25% PEG 3350, 0.2 M NH4oAC, 0.1 M BisTris pH6.5, vapor diffusion hanging drop, temperature 291K
Resolution 1.50 Å R-free 0.227
4QL1 Crystal structure of human WDR5 in complex with compound OICR-9429 Deposited 2014-06-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa）
Not recorded 35Q N-(4-(4-methylpiperazin-1-yl)-3'-(morpholinomethyl)-[1,1'-biphenyl]-3-yl)-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 UNX UNKNOWN LIGAND × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；25% PEG 3350, 0.2 M NH4oAC, 0.1 M BisTris pH6.5, vapor diffusion hanging drop, temperature 291K
Resolution 1.50 Å R-free 0.227
4QQE Crystal structure of WDR5, WD repeat domain 5 in complex with compound SGC-DS-MT-0345 Deposited 2014-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa） Fragment：UNP residues 24-334
Not recorded 37F N-[2-(4-methylpiperazin-1-yl)-5-(quinolin-3-yl)phenyl]-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 3 UNX UNKNOWN LIGAND × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；22% PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.80 Å R-free 0.218
4Y7R Crystal structure of WDR5 in complex with MYC MbIIIb peptide Deposited 2015-02-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1 M Tris 7.0, 25% PEG 8K
Resolution 1.90 Å R-free 0.188
5EAL Crystal structure of human WDR5 in complex with compound 9h Deposited 2015-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded 5ML 3-methyl-~{N}-[2-(4-methylpiperazin-1-yl)-5-quinolin-3-yl-phenyl]benzamide × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 8 UNX UNKNOWN LIGAND × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 5K MME, 0.1 M BisTris pH6.5
Resolution 1.80 Å R-free 0.211
5EAL Crystal structure of human WDR5 in complex with compound 9h Deposited 2015-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded 5ML 3-methyl-~{N}-[2-(4-methylpiperazin-1-yl)-5-quinolin-3-yl-phenyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 9 UNX UNKNOWN LIGAND × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 5K MME, 0.1 M BisTris pH6.5
Resolution 1.80 Å R-free 0.211
5EAM Crystal structure of human WDR5 in complex with compound 9o Deposited 2015-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded 5MN ~{N}-[5-(1~{H}-indol-5-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methyl-benzamide × 1 EDO 1,2-ETHANEDIOL × 1 UNX UNKNOWN LIGAND × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；25% PEG3350, 0.1M NH4SO4, 0.1 M BisTris pH6.5
Resolution 1.80 Å R-free 0.228
5EAM Crystal structure of human WDR5 in complex with compound 9o Deposited 2015-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded 5MN ~{N}-[5-(1~{H}-indol-5-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methyl-benzamide × 1 EDO 1,2-ETHANEDIOL × 4 UNX UNKNOWN LIGAND × 14 SO4 SULFATE ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；25% PEG3350, 0.1M NH4SO4, 0.1 M BisTris pH6.5
Resolution 1.80 Å R-free 0.228
5EAP Crystal structure of human WDR5 in complex with compound 9e Deposited 2015-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded 5MO N-[5-(2,3-dihydro-1-benzofuran-5-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methylbenzamide × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 5 UNX UNKNOWN LIGAND × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；28% PEG 2K MME, 0.1 M BisTris pH6.5
Resolution 1.73 Å R-free 0.241
5EAR Crystal structure of human WDR5 in complex with compound 9d Deposited 2015-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded 5MQ N-[5-(2,3-dihydro-1-benzofuran-7-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methylbenzamide × 1 EDO 1,2-ETHANEDIOL × 9 UNX UNKNOWN LIGAND × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；22% PEG 3350, 0.1M NH4SO4, 0.1 M BisTris pH5.5
Resolution 1.80 Å R-free 0.185
5EAR Crystal structure of human WDR5 in complex with compound 9d Deposited 2015-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded 5MQ N-[5-(2,3-dihydro-1-benzofuran-7-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methylbenzamide × 1 EDO 1,2-ETHANEDIOL × 10 UNX UNKNOWN LIGAND × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；22% PEG 3350, 0.1M NH4SO4, 0.1 M BisTris pH5.5
Resolution 1.80 Å R-free 0.185
5M23 Modulation of MLL1 Methyltransferase Activity Deposited 2016-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded 7DC 4-[(~{E})-[4-[[[(2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]amino]propanoyl]amino]-5-carbamimidamido-pentanoyl]amino]propanoyl]amino]methyl]phenyl]diazenyl]-~{N}-[(2~{S})-3-methyl-1-oxidanylidene-butan-2-yl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.02 M carboxylic acid 0.1 M bicine/Trizma base pH 8.5
Resolution 1.97 Å R-free 0.214
5M25 Modulation of MLL1 Methyltransferase Activity Deposited 2016-10-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded 7DU (2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]amino]propanoyl]amino]-5-carbamimidamido-~{N}-[(2~{S})-1-[[4-[(~{E})-[4-(hydroxymethyl)phenyl]diazenyl]phenyl]methylamino]-1-oxidanylidene-propan-2-yl]pentanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.02 M carboxylic acid 0.1 M bicine/Trizma base pH 8.5
Resolution 2.43 Å R-free 0.248
5SXM WDR5 in complex with MLL Win motif peptidomimetic Deposited 2016-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 23–334（312 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1M sodium citrate pH 5.6, 15% 2-propanol, and 17% PEG 4000, and 10mM ATP
Resolution 2.00 Å R-free 0.243
5SXM WDR5 in complex with MLL Win motif peptidomimetic Deposited 2016-08-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 23–334（312 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1M sodium citrate pH 5.6, 15% 2-propanol, and 17% PEG 4000, and 10mM ATP
Resolution 2.00 Å R-free 0.243
5VFC WDR5 bound to inhibitor MM-589 Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded 9BA N-{(3R,6S,9S,12R)-6-ethyl-12-methyl-9-[3-(N'-methylcarbamimidamido)propyl]-2,5,8,11-tetraoxo-3-phenyl-1,4,7,10-tetraazacyclotetradecan-12-yl}-2-methylpropanamide × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Na Bis-Tris pH 6.5, 26% PEG 8000 and 0.1 M ammonium sulfate
Resolution 1.64 Å R-free 0.174
6BYN Crystal structure of WDR5-Mb(S4) monobody complex Deposited 2017-12-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain W 31–334（304 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；28% PEG3350, 0.1 M BisTris pH 5.5
Resolution 2.69 Å R-free 0.248
6D9X Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-04-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded NA SODIUM ION × 1 FZM 2-phenyl-6,7-dihydro-5H-pyrrolo[1,2-a]imidazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.83 Å R-free 0.241
6DAI Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded DMS DIMETHYL SULFOXIDE × 2 G2V 6-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)-1-methylindoline × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.63 Å R-free 0.186
6DAK Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded G1Y N-{[3-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)phenyl]methyl}benzamide × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.60 Å R-free 0.188
6DAR Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded G2J N-(cyclopropylmethyl)-N-{[3-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)phenyl]methyl}-3-methoxybenzamide × 1 SO4 SULFATE ION × 2 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.88 Å R-free 0.195
6DAS Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded G2D N-[(1R)-6-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)-2,3-dihydro-1H-inden-1-yl]-3-methoxy-4-methylbenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.80 Å R-free 0.222
6DAS Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded G2D N-[(1R)-6-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)-2,3-dihydro-1H-inden-1-yl]-3-methoxy-4-methylbenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.80 Å R-free 0.222
6DY7 WDR5 in complex with a WIN site inhibitor Deposited 2018-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded HH7 N-[3-(2,4-dichlorophenoxy)propyl]-1H-imidazol-2-amine × 1 DMS DIMETHYL SULFOXIDE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.90 Å R-free 0.199
6DYA WDR5 in complex with a WIN site inhibitor Deposited 2018-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 30–334（305 aa）
Not recorded HHM N-[(3,5-dichlorophenyl)methyl]-3-[(1H-imidazol-1-yl)methyl]benzamide × 1 SO4 SULFATE ION × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 2.56 Å R-free 0.230
6E1Y Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-07-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded HLM N-[(1S)-1-(3-chlorophenyl)ethyl]-3-{[(4,5-dihydro-1H-imidazol-2-yl)amino]methyl}benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Bis-Tris pH 6.0 or Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.22 Å R-free 0.182
6E1Y Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design Deposited 2018-07-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded HLM N-[(1S)-1-(3-chlorophenyl)ethyl]-3-{[(4,5-dihydro-1H-imidazol-2-yl)amino]methyl}benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Bis-Tris pH 6.0 or Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.22 Å R-free 0.182
6E1Z Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity Deposited 2018-07-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded HLP 5-[(1H-imidazol-1-yl)methyl]furan-2-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.10 Å R-free 0.163
6E1Z Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity Deposited 2018-07-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded HLP 5-[(1H-imidazol-1-yl)methyl]furan-2-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.10 Å R-free 0.163
6E22 Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity Deposited 2018-07-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded HLS 3-{[(4,5-dihydro-1H-imidazol-2-yl)amino]methyl}-N-[(3,5-dimethoxyphenyl)methyl]-4-fluorobenzamide × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris pH 6.0 or Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.60 Å R-free 0.180
6E22 Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity Deposited 2018-07-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded HLS 3-{[(4,5-dihydro-1H-imidazol-2-yl)amino]methyl}-N-[(3,5-dimethoxyphenyl)methyl]-4-fluorobenzamide × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris pH 6.0 or Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.60 Å R-free 0.180
6E23 Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity Deposited 2018-07-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded HLJ N-[(3,4-dichlorophenyl)methyl]-3-(6-fluoro-2-methylpyridin-3-yl)-5-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris pH 6.0 or Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.66 Å R-free 0.209
6E23 Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity Deposited 2018-07-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded HLJ N-[(3,4-dichlorophenyl)methyl]-3-(6-fluoro-2-methylpyridin-3-yl)-5-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}benzamide × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris pH 6.0 or Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
Resolution 1.66 Å R-free 0.209
6IAM Modulating Protein-Protein Interactions with Visible Light Peptide Backbone Switches Deposited 2018-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 29–334（306 aa）
Not recorded K POTASSIUM ION × 3 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate
Resolution 1.51 Å R-free 0.170
6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain R 1–334（334 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain R 1–334（334 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIW Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain R 1–334（334 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIX Cryo-EM structure of human MLL1-NCP complex, binding mode1 Deposited 2019-07-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain R 1–334（334 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6KIZ Cryo-EM structure of human MLL1-NCP complex, binding mode2 Deposited 2019-07-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain R 1–334（334 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6OFZ Crystal structure of human WDR5 Deposited 2019-04-01 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；295 K；100 mM Bis-Tris pH5.9, 32% PEG3350, 54.6 mM Ammonium Sulfate
Resolution 1.85 Å R-free 0.250
6OI0 Crystal structure of human WDR5 in complex with L-arginine Deposited 2019-04-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded ARG ARGININE × 1 SO4 SULFATE ION × 2 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；295 K；100 mM Bis-Tris pH 5.9; 32% PEG3350, 54.6 mM Ammonium Sulfate, 0.66 mM L-arginine
Resolution 1.92 Å R-free 0.201
6OI1 Crystal structure of human WDR5 in complex with monomethyl L-arginine Deposited 2019-04-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded SO4 SULFATE ION × 1 GOL GLYCEROL × 2 NMM (2S)-2-amino-5-[(N-methylcarbamimidoyl)amino]pentanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；295 K；100mM Bis-Tris pH 5.9, 32% PEG3350, 54.6 mM Ammonium Sulfate, 0.66 mM monomethyl L-arginine
Resolution 1.68 Å R-free 0.236
6OI2 Crystal structure of human WDR5 in complex with symmetric dimethyl-L-arginine Deposited 2019-04-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded SO4 SULFATE ION × 3 GOL GLYCEROL × 3 2MR N3, N4-DIMETHYLARGININE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；295 K；100 mM Bis-Tris pH5.9, 32% PEG3350, 54.6 mM Ammonium Sulfate, 0.66 mM symmetric dimethyl-L-arginine
Resolution 1.68 Å R-free 0.223
6OI3 Crystal structure of human WDR5 in complex with monomethyl H3R2 peptide Deposited 2019-04-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded GOL GLYCEROL × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；295 K；100 mM Bis-Tris pH 5.9, 32% PEG3350, 54.6 mM Ammonium Sulfate, 1.67 mM monomethyl H3R2 peptide
Resolution 1.66 Å R-free 0.202
6PG3 WDR5delta23 bound to (2-butyl-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded OHJ (2-butyl-1H-imidazol-4-yl)methanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.182 M ammonium fluoride, 0.1 M sodium cacodylate (pH 5.79), 22.1 %w/v PEG8000
Resolution 2.04 Å R-free 0.206
6PG3 WDR5delta23 bound to (2-butyl-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded OHJ (2-butyl-1H-imidazol-4-yl)methanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.182 M ammonium fluoride, 0.1 M sodium cacodylate (pH 5.79), 22.1 %w/v PEG8000
Resolution 2.04 Å R-free 0.206
6PG4 WDR5delta32 bound to (2-methyl-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa）
Not recorded OHG (2-methyl-1H-imidazol-4-yl)methanol × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.114 M ammonium sulfate, 0.1 M bis-tris chloride (pH 6.11), 25.8 %w/v PEG8000
Resolution 1.60 Å R-free 0.176
6PG5 WDR5delta32 bound to benzyl (4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)carbamate Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa）
Not recorded OHV benzyl {4-[5-(hydroxymethyl)-1H-imidazol-2-yl]butyl}carbamate × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.215 M ammonium sulfate, 0.1 M sodium cacodylate (pH 7.06), 25.6 %w/v PEG8000
Resolution 1.99 Å R-free 0.202
6PG6 WDR5delta23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)acetamide Deposited 2019-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded SO4 SULFATE ION × 1 OH7 N-{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}acetamide × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.215 M ammonium sulfate, 0.1 M sodium cacodylate (pH 7.06), 25.6 %w/v PEG8000
Resolution 1.68 Å R-free 0.193
6PG6 WDR5delta23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)acetamide Deposited 2019-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded SO4 SULFATE ION × 1 OH7 N-{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.215 M ammonium sulfate, 0.1 M sodium cacodylate (pH 7.06), 25.6 %w/v PEG8000
Resolution 1.68 Å R-free 0.193
6PG7 WDR5delta32 bound to (2-(3-methoxy-3-phenylpropyl)-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa）
Not recorded OH4 {2-[(3S)-3-methoxy-3-phenylpropyl]-1H-imidazol-4-yl}methanol × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.17 M ammonium sulfate, 0.1 bis-tris chloride (pH 6.3), 30.5 %w/v PEG4000
Resolution 2.45 Å R-free 0.243
6PG8 WDR5delta23 bound to (2-(3-phenylpropyl)-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded OGY [2-(3-phenylpropyl)-1H-imidazol-4-yl]methanol × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.179 M ammonium sulfate, 0.1 M bis-tris chloride (pH 5.62), 28.6 %w/v PEG3350
Resolution 1.67 Å R-free 0.207
6PG8 WDR5delta23 bound to (2-(3-phenylpropyl)-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded OGY [2-(3-phenylpropyl)-1H-imidazol-4-yl]methanol × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.179 M ammonium sulfate, 0.1 M bis-tris chloride (pH 5.62), 28.6 %w/v PEG3350
Resolution 1.67 Å R-free 0.207
6PG8 WDR5delta23 bound to (2-(3-phenylpropyl)-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 22–334（313 aa）
Not recorded OGY [2-(3-phenylpropyl)-1H-imidazol-4-yl]methanol × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.179 M ammonium sulfate, 0.1 M bis-tris chloride (pH 5.62), 28.6 %w/v PEG3350
Resolution 1.67 Å R-free 0.207
6PG8 WDR5delta23 bound to (2-(3-phenylpropyl)-1H-imidazol-4-yl)methanol Deposited 2019-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 22–334（313 aa）
Not recorded OGY [2-(3-phenylpropyl)-1H-imidazol-4-yl]methanol × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.179 M ammonium sulfate, 0.1 M bis-tris chloride (pH 5.62), 28.6 %w/v PEG3350
Resolution 1.67 Å R-free 0.207
6PG9 WDR5delta23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)benzamide Deposited 2019-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded OH1 N-{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.182 M ammonium fluoride, 0.1 soidum cacodylate (pH 5.79), 22.1 %w/v PEG8000
Resolution 1.75 Å R-free 0.269
6PG9 WDR5delta23 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)benzamide Deposited 2019-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded OH1 N-{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.182 M ammonium fluoride, 0.1 soidum cacodylate (pH 5.79), 22.1 %w/v PEG8000
Resolution 1.75 Å R-free 0.269
6PGA WDR5delta32 bound to methyl (4-(4-(hydroxymethyl)-1H-imidazol-2-yl)butyl)carbamate Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa）
Not recorded OGM methyl {4-[5-(hydroxymethyl)-1H-imidazol-2-yl]butyl}carbamate × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.237 M ammonium sulfate, 0.1 M bis-tris chloride, 25.7 %w/v MPEG5000
Resolution 2.45 Å R-free 0.250
6PGB WDR5delta32 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)-2-phenylacetamide Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa） Fragment：UNP residues 32-334
Not recorded OJG N-{4-[5-(hydroxymethyl)-1H-imidazol-2-yl]butyl}-2-phenylacetamide × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.101 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 5.63, 25.8% w/v PEG4000
Resolution 1.73 Å R-free 0.217
6PGC WDR5delta32 bound to methyl benzyl(4-(4-(hydroxymethyl)-1H-imidazol-2-yl)butyl)carbamate Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa） Fragment：UNP residues 32-334
Not recorded SO4 SULFATE ION × 2 OJJ methyl benzyl{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}carbamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.237 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 6.92, 25.7% w/v MPEG5000
Resolution 1.81 Å R-free 0.248
6PGD WDR5delta32 bound to peptidomimetic Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa） Fragment：UNP residues 32-334
Not recorded OK4 N-acetyl-L-alanyl-5-[5-(hydroxymethyl)-1H-imidazol-2-yl]-L-norvalyl-L-valinamide × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.233 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 6.02, 26% w/v PEG8000
Resolution 1.50 Å R-free 0.167
6PGE WDR5delta32 bound to ethyl 3-(4-(hydroxymethyl)-1H-imidazol-2-yl)propanoate Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa） Fragment：UNP residues 32-334
Not recorded OJM ethyl 3-[4-(hydroxymethyl)-1H-imidazol-2-yl]propanoate × 1 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.024 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 5.64, 26.3% w/v PEG4000
Resolution 1.76 Å R-free 0.213
6PGF WDR5delta32 bound to N-(4-(4-(hydroxymethyl)-1H-imidazol-2-yl)butyl)acrylamide Deposited 2019-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa） Fragment：UNP residues 32-334
Not recorded OJP N-{4-[4-(hydroxymethyl)-1H-imidazol-2-yl]butyl}prop-2-enamide × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；281 K；0.16 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 6.1, 30.1% w/v PEG8000
Resolution 1.54 Å R-free 0.170
6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain B 22–334（313 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
6PWW Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 22–334（313 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6U5M Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q0S 5-bromo-2-hydroxy-N-[3-(methylsulfonyl)-5-(pentafluoro-lambda~6~-sulfanyl)phenyl]benzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, ammonium acetate, PEG 3350
Resolution 1.80 Å R-free 0.186
6U5M Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q0S 5-bromo-2-hydroxy-N-[3-(methylsulfonyl)-5-(pentafluoro-lambda~6~-sulfanyl)phenyl]benzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, ammonium acetate, PEG 3350
Resolution 1.80 Å R-free 0.186
6U5Y Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q0M 3-{[(5-bromo-3-chloro-2-hydroxyphenyl)sulfonyl]amino}-5-(1-cyanocyclobutyl)-2-hydroxy-N-methylbenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris pH 6.5, 0.2 M ammonium acetate, 28% PEG 3350
Resolution 1.53 Å R-free 0.177
6U5Y Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q0M 3-{[(5-bromo-3-chloro-2-hydroxyphenyl)sulfonyl]amino}-5-(1-cyanocyclobutyl)-2-hydroxy-N-methylbenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris pH 6.5, 0.2 M ammonium acetate, 28% PEG 3350
Resolution 1.53 Å R-free 0.177
6U6W Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded Q0Y 5-bromo-N-(5-chloro-2-hydroxyphenyl)-2-methoxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris pH 6.5, 0.2M ammonium acetate, PEG3350
Resolution 1.20 Å R-free 0.179
6U6W Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa）
Not recorded Q0Y 5-bromo-N-(5-chloro-2-hydroxyphenyl)-2-methoxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris pH 6.5, 0.2M ammonium acetate, PEG3350
Resolution 1.20 Å R-free 0.179
6U80 Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded Q1J 5-bromo-N-(4-hydroxy[1,1'-biphenyl]-3-yl)-2-methoxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium Acetate, PEG 3350
Resolution 1.55 Å R-free 0.203
6U80 Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa）
Not recorded Q1J 5-bromo-N-(4-hydroxy[1,1'-biphenyl]-3-yl)-2-methoxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium Acetate, PEG 3350
Resolution 1.55 Å R-free 0.203
6U8B Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa）
Not recorded Q1M 3-{[(5-bromo-2-methoxyphenyl)sulfonyl]amino}-5-chloro-2-hydroxybenzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, ammonium acetate, PEG 3350
Resolution 1.26 Å R-free 0.159
6U8B Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa）
Not recorded Q1M 3-{[(5-bromo-2-methoxyphenyl)sulfonyl]amino}-5-chloro-2-hydroxybenzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, ammonium acetate, PEG 3350
Resolution 1.26 Å R-free 0.159
6U8L Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q1P 3-{[(5-bromo-2-hydroxyphenyl)sulfonyl]amino}-5-cyclopropyl-6-fluoro-2-hydroxybenzoic acid × 1 Q1S N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]isoquinolin-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium acetate, PEG 3350
Resolution 1.57 Å R-free 0.176
6U8L Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q1P 3-{[(5-bromo-2-hydroxyphenyl)sulfonyl]amino}-5-cyclopropyl-6-fluoro-2-hydroxybenzoic acid × 1 Q1S N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]isoquinolin-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium acetate, PEG 3350
Resolution 1.57 Å R-free 0.176
6U8O Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction Deposited 2019-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q1G 5-bromo-N-[5-(1-cyanocyclobutyl)-2-hydroxyphenyl]-2-hydroxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, ammonium acetate, PEG 3350
Resolution 1.60 Å R-free 0.184
6UCS Discovery and Structure-Based optimization of potent and selective WDR5 inhibitors containing a dihydroisoquinolinone bicyclic core Deposited 2019-09-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded Q41 2-amino-3-{[(5P)-2-[(3,5-dimethoxyphenyl)methyl]-5-(4-fluoro-2-methylphenyl)-1-oxo-1,2,3,4-tetrahydroisoquinolin-7-yl]methyl}-1-methyl-1H-imidazol-3-ium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium Acetate, PEG 3350
Resolution 1.85 Å R-free 0.194
6UCS Discovery and Structure-Based optimization of potent and selective WDR5 inhibitors containing a dihydroisoquinolinone bicyclic core Deposited 2019-09-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded Q41 2-amino-3-{[(5P)-2-[(3,5-dimethoxyphenyl)methyl]-5-(4-fluoro-2-methylphenyl)-1-oxo-1,2,3,4-tetrahydroisoquinolin-7-yl]methyl}-1-methyl-1H-imidazol-3-ium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium Acetate, PEG 3350
Resolution 1.85 Å R-free 0.194
6UFX WD repeat-containing protein 5 complexed with N-[(3,5-dimethoxyphenyl)methyl]-4'-fluoro-5-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}-2'-methyl[1,1'-biphenyl]-3-carboxamide (compound 13) Deposited 2019-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–334（303 aa） Fragment：UNP residues 32-334
Not recorded Q6S N-[(3,5-dimethoxyphenyl)methyl]-4'-fluoro-5-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}-2'-methyl[1,1'-biphenyl]-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Bis-Tris or HEPES or Tris-HCl, pH 6.0-8.0, 0.2 M ammonium acetate, 20-30% PEG3350
Resolution 2.02 Å R-free 0.208
6UHY WDR5 in complex with Myc site fragment inhibitor Deposited 2019-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q8G 1-cyclohexyl-1H-benzimidazole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350.
Resolution 1.26 Å R-free 0.181
6UHY WDR5 in complex with Myc site fragment inhibitor Deposited 2019-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q8G 1-cyclohexyl-1H-benzimidazole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350.
Resolution 1.26 Å R-free 0.181
6UHZ WDR5 in complex with Myc site fragment inhibitor Deposited 2019-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q8D 1-cyclohexyl-1H-benzotriazole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% PEG3350
Resolution 1.26 Å R-free 0.176
6UHZ WDR5 in complex with Myc site fragment inhibitor Deposited 2019-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q8D 1-cyclohexyl-1H-benzotriazole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% PEG3350
Resolution 1.26 Å R-free 0.176
6UIF Discovery of fragment-inspired heterocyclic benzenesulfonmides as inhibitors of the WDR5-MYC interaction Deposited 2019-09-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q8P 4-{[(5-bromo-3-chloro-2-hydroxyphenyl)sulfonyl]amino}-1-cyclopentyl-N-methyl-1H-imidazole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium acetate, PEG 3350
Resolution 1.60 Å R-free 0.194
6UIF Discovery of fragment-inspired heterocyclic benzenesulfonmides as inhibitors of the WDR5-MYC interaction Deposited 2019-09-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q8P 4-{[(5-bromo-3-chloro-2-hydroxyphenyl)sulfonyl]amino}-1-cyclopentyl-N-methyl-1H-imidazole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium acetate, PEG 3350
Resolution 1.60 Å R-free 0.194
6UIK Discovery of fragment-inspired heterocyclic benzenesulfonmides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q8M 5-bromo-3-chloro-N-(1-cyclopentyl-1H-imidazol-4-yl)-2-hydroxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris 6.5, 0.2 M Ammonium Acetate, 28% PEG 3350
Resolution 1.60 Å R-free 0.182
6UIK Discovery of fragment-inspired heterocyclic benzenesulfonmides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q8M 5-bromo-3-chloro-N-(1-cyclopentyl-1H-imidazol-4-yl)-2-hydroxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris 6.5, 0.2 M Ammonium Acetate, 28% PEG 3350
Resolution 1.60 Å R-free 0.182
6UJ4 Discovery of fragment-inspired heterocyclic benzenesulfonmides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–334（304 aa）
Not recorded Q8S 5-bromo-3-chloro-N-(1-cyclopentyl-2-methyl-1H-imidazol-4-yl)-2-hydroxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris 6.5, 0.2 M Ammonium acetate, 28% PEG 3350
Resolution 1.53 Å R-free 0.177
6UJ4 Discovery of fragment-inspired heterocyclic benzenesulfonmides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 31–334（304 aa）
Not recorded Q8S 5-bromo-3-chloro-N-(1-cyclopentyl-2-methyl-1H-imidazol-4-yl)-2-hydroxybenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris 6.5, 0.2 M Ammonium acetate, 28% PEG 3350
Resolution 1.53 Å R-free 0.177
6UJH Discovery of fragment-inspired heterocyclic benzenesulfonamides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded QBS (2R)-2-(4-chlorophenyl)-3-oxobutanenitrile × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes, 0.2 M ammonium acetate, 32% PEG3350
Resolution 1.49 Å R-free 0.169
6UJH Discovery of fragment-inspired heterocyclic benzenesulfonamides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded QBS (2R)-2-(4-chlorophenyl)-3-oxobutanenitrile × 1 SO4 SULFATE ION × 1 DMS DIMETHYL SULFOXIDE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes, 0.2 M ammonium acetate, 32% PEG3350
Resolution 1.49 Å R-free 0.169
6UJJ Discovery of fragment-inspired heterocyclic benzenesulfonamides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded QBP 5-[4-(trifluoromethyl)phenyl]-1H-tetrazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Hepes, 0.2 M ammonium acetate, 32% PEG3350
Resolution 1.73 Å R-free 0.190
6UJL Discovery of fragment-inspired heterocyclic benzenesulfonamides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded QBM 6-methyl-3-(propylsulfanyl)-1,2,4-triazin-5-ol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Hepes, 0.2 M ammonium acetate, 32% PEG3350
Resolution 1.60 Å R-free 0.183
6UOZ Discovery of fragment-inspired heterocyclic benzenesulfonmides as inhibitors of the WDR5-MYC interaction Deposited 2019-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–334（304 aa）
Chain B 31–334（304 aa）
Not recorded QF1 5-bromo-3-chloro-N-[1-cyclopentyl-2-(methylsulfonyl)-1H-imidazol-4-yl]-2-hydroxybenzene-1-sulfonamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, ammonium acetate, PEG 3350
Resolution 1.53 Å R-free 0.169
6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 22–334（313 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6W5N Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Deposited 2020-03-13 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 22–334（313 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
6WJQ Crystal structure of WDR5 in complex with the WIN peptide of PDPK1 Deposited 2020-04-14 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；PEG 3350, Ammonium Acetate, Bis-tris
Resolution 2.71 Å R-free 0.252
6WJQ Crystal structure of WDR5 in complex with the WIN peptide of PDPK1 Deposited 2020-04-14 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；PEG 3350, Ammonium Acetate, Bis-tris
Resolution 2.71 Å R-free 0.252
7AXP Structural characterisation of WDR5:CS-VIP8 interaction in cis state 2 Deposited 2020-11-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate
Resolution 2.43 Å R-free 0.331
7AXQ Structure of the cryo-trapped WDR5:CS-VIP8 cocrystal after illumination at 405 nm and 180 K Deposited 2020-11-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate
Resolution 1.56 Å R-free 0.200
7AXS Structural characterisation of WDR5:CS-VIP8 interaction in cis state 1 Deposited 2020-11-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate
Resolution 1.88 Å R-free 0.235
7AXU Structure of WDR5:CS-VIP8 cocrystal after illumination in situ Deposited 2020-11-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate
Resolution 1.68 Å R-free 0.193
7AXX Structure of WDR5:CS-VIP8 crystal after illumination at 405 nm and room temperature Deposited 2020-11-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277.15 K；10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate
Resolution 1.79 Å R-free 0.214
7BCY X-ray structure of WDR5delta24 bound to the Kaposi's sarcoma herpesvirus LANA win motif peptide Deposited 2020-12-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 25–334（310 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；294 K；100 mM Bis-Tris pH 5.5, 50 mM (NH4)2SO4, 25% PEG3350
Resolution 1.50 Å R-free 0.227
7BCY X-ray structure of WDR5delta24 bound to the Kaposi's sarcoma herpesvirus LANA win motif peptide Deposited 2020-12-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 25–334（310 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；294 K；100 mM Bis-Tris pH 5.5, 50 mM (NH4)2SO4, 25% PEG3350
Resolution 1.50 Å R-free 0.227
7BED X-ray structure of WDR5 bound to the WDR5 win motif peptide Deposited 2020-12-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Chain B 1–334（334 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；26% PEG 3350, 100mM Bis-Tris pH 5.5, 50mM (NH4)2SO4,WDR5 at 14,65 mg/ml with 2:1 (protein:well) drop ratio.
Resolution 1.26 Å R-free 0.171
7CFP Crystal structure of WDR5 in complex with a H3Q5ser peptide Deposited 2020-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Not recorded SRO SEROTONIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；0.1% Octylglucoside, 0.1M Sodium citrate tribasic dihydrate pH 5.5, 22% PEG 3350
Resolution 1.60 Å R-free 0.199
7CFQ Crystal structure of WDR5 in complex with H3K4me3Q5ser peptide Deposited 2020-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Not recorded GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1 SRO SEROTONIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；0.15M ammonium sulfate, 0.1M MES pH 5.5, 25% PEG 4000, 2% PEG 3350
Resolution 1.60 Å R-free 0.190
7DNO Characterization of Peptide Ligands Against WDR5 Isolated Using Phage Display Technique Deposited 2020-12-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 24–334（311 aa）
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1 M BisTris pH 6.0, 0.2M ammonium acetate, 20-30% PEG3350
Resolution 2.03 Å R-free 0.227
7JTO Crystal structure of Protac MS33 in complex with the WD repeat-containing protein 5 and pVHL:ElonginC:ElonginB Deposited 2020-08-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 31–334（304 aa）
Not recorded SCN THIOCYANATE ION × 4 EDO 1,2-ETHANEDIOL × 5 VKA 3-methyl-N-(11-{[2-(4-{[4'-(4-methylpiperazin-1-yl)-3'-{[6-oxo-4-(trifluoromethyl)-5,6-dihydropyridine-3-carbonyl]amino}[1,1'-biphenyl]-3-yl]methyl}piperazin-1-yl)ethyl]amino}-11-oxoundecanoyl)-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 GOL GLYCEROL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.1 M HEPES sodium, pH 7.5-8.0, 1.3-1.6 M sodium thiocyanate, 15-20% PEG3350
Resolution 1.70 Å R-free 0.225
7JTP Crystal structure of Protac MS67 in complex with the WD repeat-containing protein 5 and pVHL:ElonginC:ElonginB Deposited 2020-08-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 31–334（304 aa）
Not recorded GOL GLYCEROL × 1 X6M N-(6-fluoro-3'-{[6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carbonyl]amino}-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-carbonyl)glycyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.1 M Tris, pH 8.5, 30% PEG300
Resolution 2.12 Å R-free 0.224
7MBM Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Deposited 2021-04-01 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 22–334（313 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.76 Å
7MBN Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Deposited 2021-04-01 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 22–334（313 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
7Q2J Quaternary Complex of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC Homer Deposited 2021-10-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 24–334（311 aa）
Not recorded 8KH N-[5-[4-[[5-[[(2S)-3,3-dimethyl-1-[(2S,4R)-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-5-oxidanylidene-pentyl]carbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanylidene-4-(trifluoromethyl)-1H-pyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；21% PEG 3350 0.4 M KSCN 0.1 M HEPES 6.8
Resolution 2.50 Å R-free 0.293
7U9Y WDR5 bound to 2-(3,5-dimethoxybenzyl)-7-((2-methyl-1H-imidazol-1-yl)methyl)-5-(1-methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl)-3,4-dihydroisoquinolin-1(2H)-one Deposited 2022-03-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 30–334（305 aa）
Not recorded BEN BENZAMIDINE × 1 M4U (5P)-2-[(3,5-dimethoxyphenyl)methyl]-7-[(2-methyl-1H-imidazol-1-yl)methyl]-5-[1-methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-3,4-dihydroisoquinolin-1(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；BIS-Tris, ammonium acetate, PEG 3350, benzamidine
Resolution 1.90 Å R-free 0.189
7UAS Discovery of Potent Orally Bioavailable WD Repeat Domain 5 (WDR5) Inhibitors Using a Pharmacophore-Based Optimization Deposited 2022-03-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded MBU (5P)-2-[(S)-cyclopropyl(4-methylpyridin-2-yl)methyl]-5-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-7-[(2-methyl-1H-imidazol-1-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium Acetate, PEG 3350
Resolution 1.81 Å R-free 0.175
7UAS Discovery of Potent Orally Bioavailable WD Repeat Domain 5 (WDR5) Inhibitors Using a Pharmacophore-Based Optimization Deposited 2022-03-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded MBU (5P)-2-[(S)-cyclopropyl(4-methylpyridin-2-yl)methyl]-5-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-7-[(2-methyl-1H-imidazol-1-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Bis-Tris, Ammonium Acetate, PEG 3350
Resolution 1.81 Å R-free 0.175
7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain L 2–334（333 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
7WVK Crystal structure of human WDR5 in complex with compound 19 Deposited 2022-02-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded 6IQ 1-[2,5-bis(chloranyl)phenyl]sulfonylbenzimidazole × 1 GOL GLYCEROL × 4 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1M Bis-Tris, 0.2 M NH4OAC, 30% PEG3350
Resolution 1.42 Å R-free 0.182
8BB2 Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #2) Deposited 2022-10-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 33–334（302 aa）
Not recorded SCN THIOCYANATE ION × 5 Q3X ~{N}-[5-[4-[2-[2-[2-[2-[3-[[3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanylidene-4-(trifluoromethyl)-3~{H}-pyridine-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；21-28% PEG 3350 0.4-1 M KSCN 0.1 M HEPES 6.8
Resolution 2.05 Å R-free 0.237
8BB3 Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #1) Deposited 2022-10-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 33–334（302 aa）
Not recorded SCN THIOCYANATE ION × 15 EDO 1,2-ETHANEDIOL × 13 P6G HEXAETHYLENE GLYCOL × 1 Q3X ~{N}-[5-[4-[2-[2-[2-[2-[3-[[3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanylidene-4-(trifluoromethyl)-3~{H}-pyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；21-26% PEG 3350 0.4-1 M KSCN 0.1 M HEPES
Resolution 1.80 Å R-free 0.227
8BB4 Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with C3 linker Deposited 2022-10-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain Q 33–334（302 aa）
Not recorded Q3R ~{N}-[5-[4-[[4-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-4-oxidanylidene-butyl]carbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanyl-4-(trifluoromethyl)pyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；293 K；21-28% PEG 3350 0.4 M KSCN 0.1 M HEPES pH 6.8
Resolution 2.80 Å R-free 0.279
8BB5 Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with Aryl linker Deposited 2022-10-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 33–334（302 aa）
Not recorded SCN THIOCYANATE ION × 10 Q43 ~{N}-[5-[4-[[4-[2-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-2-oxidanylidene-ethyl]phenyl]methylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanyl-4-(trifluoromethyl)pyridine-3-carboxamide × 1 EDO 1,2-ETHANEDIOL × 4 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；21% PEG 3350, 0.4-1 M KSCN 0.1 M HEPES pH 6.8
Resolution 2.20 Å R-free 0.248
8DU4 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Deposited 2022-07-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain L 2–334（333 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
8E9F WD repeat-containing protein 5 complexed with 4-(7-((1H-imidazol-1-yl)methyl)-5-(1-methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl)-1-oxo-3,4-dihydroisoquinolin-2(1H)-yl)-6-ethyl-N-methylquinoline-8-carboxamide (compound 10) Deposited 2022-08-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 30–334（305 aa）
Not recorded BEN BENZAMIDINE × 1 UY9 6-ethyl-4-[(5P)-7-[(1H-imidazol-1-yl)methyl]-5-[1-methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-1-oxo-3,4-dihydroisoquinolin-2(1H)-yl]-N-methylquinoline-8-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；BIS-Tris, ammonium acetate, PEG 3350, benzamidine
Resolution 1.55 Å R-free 0.184
8F1G Crystal structure of human WDR5 in complex with compound WM662 Deposited 2022-11-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded X8N (2S)-2-({(2S)-3-(3'-chloro[1,1'-biphenyl]-4-yl)-1-oxo-1-[(1H-tetrazol-5-yl)amino]propan-2-yl}oxy)propanoic acid × 1 GOL GLYCEROL × 4 SO4 SULFATE ION × 1 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH=7.4, 25 mM ammonium sulfate, 24% w/v Polyethylene glycol 3350
Resolution 2.14 Å R-free 0.249
8F1G Crystal structure of human WDR5 in complex with compound WM662 Deposited 2022-11-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded X8N (2S)-2-({(2S)-3-(3'-chloro[1,1'-biphenyl]-4-yl)-1-oxo-1-[(1H-tetrazol-5-yl)amino]propan-2-yl}oxy)propanoic acid × 1 GOL GLYCEROL × 3 SO4 SULFATE ION × 1 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH=7.4, 25 mM ammonium sulfate, 24% w/v Polyethylene glycol 3350
Resolution 2.14 Å R-free 0.249
8F93 WDR5 covalently modified at Y228 by (R)-2-SF Deposited 2022-11-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: monomeric
Chain A 22–334（313 aa）
Chain B 22–334（313 aa）
Not recorded XKN 3-ethynyl-5-{[(3R)-4-{1-[(2-methoxyphenyl)methyl]-1H-benzimidazole-5-carbonyl}-3-methylpiperazin-1-yl]methyl}benzene-1-sulfonyl fluoride × 2 GOL GLYCEROL × 4 SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium sulfate, 0.1 M MES pH 6.5, 20% w/v PEG 8000
Resolution 2.30 Å R-free 0.253
8F93 WDR5 covalently modified at Y228 by (R)-2-SF Deposited 2022-11-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: monomeric
Chain A 22–334（313 aa）
Chain B 22–334（313 aa）
Not recorded XKN 3-ethynyl-5-{[(3R)-4-{1-[(2-methoxyphenyl)methyl]-1H-benzimidazole-5-carbonyl}-3-methylpiperazin-1-yl]methyl}benzene-1-sulfonyl fluoride × 2 GOL GLYCEROL × 4 SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Ammonium sulfate, 0.1 M MES pH 6.5, 20% w/v PEG 8000
Resolution 2.30 Å R-free 0.253
8G3C Crystal structure of human WDR5 in complex with N-[(2'-cyano[1,1'-biphenyl]-4-yl)methyl]-3-hydroxy-6-methyl-4-oxo-4H-pyran-2-carboxamide (compound 1, WDR5-MYC PPI inhibitor) Deposited 2023-02-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded YJN N-[(2'-cyano[1,1'-biphenyl]-4-yl)methyl]-3-hydroxy-6-methyl-4-oxo-4H-pyran-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；20% PEG3350, 0.2 M potassium acetate
Resolution 1.80 Å R-free 0.224
8G3E Crystal structure of human WDR5 in complex with (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide (compound 2, WDR5-MYC inhibitor) Deposited 2023-02-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded YJR (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；23.5% PEG3350, 0.21 M ammonium sulfate, 0.1 M HEPES, pH 7.5
Resolution 1.33 Å R-free 0.170
8G3E Crystal structure of human WDR5 in complex with (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide (compound 2, WDR5-MYC inhibitor) Deposited 2023-02-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded YJR (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；23.5% PEG3350, 0.21 M ammonium sulfate, 0.1 M HEPES, pH 7.5
Resolution 1.33 Å R-free 0.170
8HMX WDR5 in complex with histone H3Q5his peptide Deposited 2022-12-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 31–334（304 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium citrate tribasic dihydrate (pH 5.5), 22% polyethylene glycol (PEG) 3350, and 0.1% n-Octyl-beta-D-glucoside
Resolution 1.70 Å R-free 0.193
8Q1N Cyclic peptide binder of the WBM-site of WDR5 Deposited 2023-08-01 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Li3-Citrate, 20 w/v% PEG3350
Resolution 1.84 Å R-free 0.243
8Q1N Cyclic peptide binder of the WBM-site of WDR5 Deposited 2023-08-01 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Li3-Citrate, 20 w/v% PEG3350
Resolution 1.84 Å R-free 0.243
8T5I Crystal structure of human WDR5 in complex with MR4397 Deposited 2023-06-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded ZHF N-[(2S)-1-(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)-1-oxopentan-2-yl]-3-[(1H-imidazol-1-yl)methyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 3 UNX UNKNOWN LIGAND × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；25% PEG3350, 0.2 M (NH4)2SO4, 0.1M BTP pH 7.0
Resolution 1.70 Å R-free 0.232
8T5I Crystal structure of human WDR5 in complex with MR4397 Deposited 2023-06-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded ZHF N-[(2S)-1-(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)-1-oxopentan-2-yl]-3-[(1H-imidazol-1-yl)methyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 5 UNX UNKNOWN LIGAND × 1 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；25% PEG3350, 0.2 M (NH4)2SO4, 0.1M BTP pH 7.0
Resolution 1.70 Å R-free 0.232
8UJY Crystal structure of human WD repeat-containing protein 5 in complex with 4-(3,5-dimethoxybenzyl)-9-(4-fluoro-2-methylphenyl)-7-((2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl)methyl)-3,4-dihydrobenzo[f][1,4]oxazepin-5(2H)-one (compound 8) Deposited 2023-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa） Fragment：UNP residues 23-334
Chain B 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded VV3 (9P)-4-[(3,5-dimethoxyphenyl)methyl]-9-(4-fluoro-2-methylphenyl)-7-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}-3,4-dihydro-1,4-benzoxazepin-5(2H)-one × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1 M Bis-Tris pH 7.0, 0.2 M ammonium acetate, 25% PEG3350
Resolution 2.01 Å R-free 0.232
8WXQ Structure of WDR5 in complex with WIN motif containing MBD3C Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M HEPES (pH 7.5), 18% PEG 600
Resolution 1.90 Å R-free 0.209
8WXQ Structure of WDR5 in complex with WIN motif containing MBD3C Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M HEPES (pH 7.5), 18% PEG 600
Resolution 1.90 Å R-free 0.209
8WXR Structure of WDR5 in complex with WIN motif containing MBD3C F47A Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M potassium dihydrogen phosphate, 20% PEG 3350
Resolution 2.08 Å R-free 0.199
8WXR Structure of WDR5 in complex with WIN motif containing MBD3C F47A Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M potassium dihydrogen phosphate, 20% PEG 3350
Resolution 2.08 Å R-free 0.199
8WXT Structure of WDR5 in complex with WIN motif containing MBD3C R45E/V46G Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.2 M imidazole malate, pH 5.5, 33% PEG 600
Resolution 1.83 Å R-free 0.179
8WXU Structure of WDR5 in complex with WIN motif containing MBD3C C44S/R45E/V46G Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M lithium chloride, 20% PEG 3350
Resolution 2.37 Å R-free 0.233
8WXV Structure of WDR5 in complex with WIN motif containing SET1B Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.1 M Bis-Tris, pH 5.5, 25% PEG 3350
Resolution 2.40 Å R-free 0.205
8WXV Structure of WDR5 in complex with WIN motif containing SET1B Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.1 M Bis-Tris, pH 5.5, 25% PEG 3350
Resolution 2.40 Å R-free 0.205
8WXX Structure of WDR5 in complex with WIN motif containing SET1B E1750R/G1751V Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.1 M sodium citrate, pH 5.5, 16% PEG 4000, 10% 2-propanol
Resolution 2.10 Å R-free 0.212
8WXX Structure of WDR5 in complex with WIN motif containing SET1B E1750R/G1751V Deposited 2023-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.1 M sodium citrate, pH 5.5, 16% PEG 4000, 10% 2-propanol
Resolution 2.10 Å R-free 0.212
8X3R Crystal structure of human WDR5 in complex with WDR5 Deposited 2023-11-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Chain B 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M magnesium formate dihydrate, 15% w/v polyethylene glycol 3350
Resolution 1.76 Å R-free 0.205
8X3S Crystal structure of human WDR5 in complex with PTEN Deposited 2023-11-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 21–334（314 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M lithium sulfate monohydrate, 0.1 M HEPES at pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 1.87 Å R-free 0.259
9B9H Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40333 Deposited 2024-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded A1AM2 N-{(1P)-5'-({(17E)-18-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-16-oxo-3,6,9,12-tetraoxa-15-azaoctadec-17-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；5% w/v 1-ethyl-3-methylimidazolium ethyl sulfate, 15% w/v polyethylene glycol 20,000, pH 7.9
Resolution 2.06 Å R-free 0.229
9B9T Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40407 Deposited 2024-04-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded A1ANM N-{(1P)-5'-[(17-{(4P)-4-[(2P)-4-{[(1R)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-1H-pyrazol-1-yl}-16-oxo-3,6,9,12-tetraoxa-15-azaheptadecan-1-yl)carbamoyl]-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M sodium acetate trihydrate, pH 4.6, 2.0 M sodium formate
Resolution 2.05 Å R-free 0.196
9B9W Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40792 Deposited 2024-04-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded A1ANN (4P)-N-[(1R)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(25E)-1-{(1P)-6-fluoro-3'-[4-fluoro-2-(trifluoromethyl)benzamido]-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-1,24-dioxo-5,8,11,14,17,20-hexaoxa-2,23-diazahexacos-25-en-26-yl]-1H-pyrrole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；35% v/v tacsimate, pH 7.0
Resolution 1.92 Å R-free 0.183
9BA2 Crystal structure of the binary complex of DCAF1 and WDR5 Deposited 2024-04-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded IMD IMIDAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.2 M imidazole, pH 7.4, 20% w/v polyethylene glycol 4,000
Resolution 2.97 Å R-free 0.266
9D5Z Crystal structure of the human WDR5 in complex with LH168 compound Deposited 2024-08-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded A1A16 (3P)-N-[(2S)-1-(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)-1-oxopentan-2-yl]-3-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-5-[(1H-imidazol-1-yl)methyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M Ammonium formate
Resolution 1.70 Å R-free 0.189
9D5Z Crystal structure of the human WDR5 in complex with LH168 compound Deposited 2024-08-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–334（311 aa） Fragment：UNP residues 23-334
Not recorded A1A16 (3P)-N-[(2S)-1-(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)-1-oxopentan-2-yl]-3-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-5-[(1H-imidazol-1-yl)methyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG3350, 0.2 M Ammonium formate
Resolution 1.70 Å R-free 0.189
9DLW Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41114 Deposited 2024-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded A1BAF N-{(1P)-5'-({(32E)-33-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-31-oxo-3,6,9,12,15,18,21,24,27-nonaoxa-30-azatritriacont-32-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；294 K；1.8 M Sodium phosphate monobasic monohydrate, potassium phosphate dibasic / pH 6.9
Resolution 2.07 Å R-free 0.242
9IY5 WDR5 inhibitor complex Deposited 2024-07-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；Bis-tris pH 5.5 25% PEG 4000
Resolution 1.80 Å R-free 0.255
9IY5 WDR5 inhibitor complex Deposited 2024-07-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–334（334 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；Bis-tris pH 5.5 25% PEG 4000
Resolution 1.80 Å R-free 0.255
9J20 Structure of WDR5 in complex with KIF2A Deposited 2024-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M HEPES (pH 7.5) and 18% PEG 600
Resolution 1.85 Å R-free 0.206
9J20 Structure of WDR5 in complex with KIF2A Deposited 2024-08-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M HEPES (pH 7.5) and 18% PEG 600
Resolution 1.85 Å R-free 0.206
9JWV Structure of WDR5 Y191F in complex with WIN motif containing Kif2A Deposited 2024-10-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Mutation：Y191F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M HEPES (pH 7.5), 18% PEG 600
Resolution 1.80 Å R-free 0.211
9JWV Structure of WDR5 Y191F in complex with WIN motif containing Kif2A Deposited 2024-10-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Mutation：Y191F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M HEPES (pH 7.5), 18% PEG 600
Resolution 1.80 Å R-free 0.211
9KD4 Structure of WDR5 in complex with WIN motif containing Kif2A 114-120 Deposited 2024-11-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium acetate, 0.1 M Sodium acetate pH=4, 15% PEG 4000
Resolution 1.64 Å R-free 0.204
9KD4 Structure of WDR5 in complex with WIN motif containing Kif2A 114-120 Deposited 2024-11-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium acetate, 0.1 M Sodium acetate pH=4, 15% PEG 4000
Resolution 1.64 Å R-free 0.204
9KD5 Structure of WDR5 in complex with WIN motif containing Kif2A S121G Deposited 2024-11-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M imidazole malate, pH=5.5, 24% PEG 600
Resolution 1.80 Å R-free 0.216
9KD5 Structure of WDR5 in complex with WIN motif containing Kif2A S121G Deposited 2024-11-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M imidazole malate, pH=5.5, 24% PEG 600
Resolution 1.80 Å R-free 0.216
9KFM Structure of WDR5 in complex with WIN motif containing EMBOW Deposited 2024-11-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium cacodylate, pH 5.5, 25% (w/v) PEG 4000
Resolution 1.80 Å R-free 0.201
9KFM Structure of WDR5 in complex with WIN motif containing EMBOW Deposited 2024-11-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium cacodylate, pH 5.5, 25% (w/v) PEG 4000
Resolution 1.80 Å R-free 0.201
9KFN Structure of WDR5 in complex with mutated EMBOW T3V Deposited 2024-11-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M imidazole malate, pH 8.5, 12.5 % (w/v) PEG 10000.
Resolution 2.80 Å R-free 0.241
9KFO Structure of WDR5 in complex with mutated EMBOW Deposited 2024-11-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium HEPES, pH 7.0, 15 % (w/v) PEG 4000.
Resolution 2.20 Å R-free 0.190
9KQS Crystal structure of WDR5 in complex with peptide MRTEPRPPAP of EMBOW Deposited 2024-11-26 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291.15 K；0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.72 Å R-free 0.210
9L0T Structure of WDR5 in complex with WIN motif containing RBM15 Deposited 2024-12-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M imidazole malate, pH 6.0, and 15 % (w/v) PEG 4000
Resolution 2.05 Å R-free 0.245
9L0T Structure of WDR5 in complex with WIN motif containing RBM15 Deposited 2024-12-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M imidazole malate, pH 6.0, and 15 % (w/v) PEG 4000
Resolution 2.05 Å R-free 0.245
9L0V Structure of WDR5 in complex with WIN motif containing ZSCAN10 Deposited 2024-12-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium citrate, pH 4.5, and 20 % (w/v) PEG 4000
Resolution 2.00 Å R-free 0.220
9LWY Crystal structure of human WDR5 in complex with compound 4 Deposited 2025-02-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded GOL GLYCEROL × 1 A1EMB 4-[[2-(6-fluoranyl-2-methyl-pyridin-3-yl)-6-(5-methyl-1,3-thiazol-2-yl)pyridin-4-yl]methyl]-1-methyl-imidazol-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, Bis-Tris, ammonium acetate
Resolution 1.55 Å R-free 0.191
9NCT Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded A1BW7 4-({6-cyclopropyl-8-[(2-methyl-1H-imidazol-1-yl)methyl]-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazol-3-yl}methyl)-2-methoxybenzonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；Ammonium Acetate, PEG 3350, Bis-TRS, TRIS, or HEPES
Resolution 2.11 Å R-free 0.228
9NCT Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded A1BW7 4-({6-cyclopropyl-8-[(2-methyl-1H-imidazol-1-yl)methyl]-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazol-3-yl}methyl)-2-methoxybenzonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；Ammonium Acetate, PEG 3350, Bis-TRS, TRIS, or HEPES
Resolution 2.11 Å R-free 0.228
9NCV Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded A1BW8 (6P)-6-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-3-[(4-fluoro-3-methylphenyl)methyl]-8-[(2-methyl-1H-imidazol-1-yl)methyl]-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG3350, Bis-TRIS, TRIS, HEPES
Resolution 1.58 Å R-free 0.287
9NCV Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded A1BW8 (6P)-6-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-3-[(4-fluoro-3-methylphenyl)methyl]-8-[(2-methyl-1H-imidazol-1-yl)methyl]-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG3350, Bis-TRIS, TRIS, HEPES
Resolution 1.58 Å R-free 0.287
9NCV Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 22–334（313 aa）
Not recorded A1BW8 (6P)-6-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-3-[(4-fluoro-3-methylphenyl)methyl]-8-[(2-methyl-1H-imidazol-1-yl)methyl]-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG3350, Bis-TRIS, TRIS, HEPES
Resolution 1.58 Å R-free 0.287
9NCV Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 22–334（313 aa）
Not recorded A1BW8 (6P)-6-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-3-[(4-fluoro-3-methylphenyl)methyl]-8-[(2-methyl-1H-imidazol-1-yl)methyl]-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG3350, Bis-TRIS, TRIS, HEPES
Resolution 1.58 Å R-free 0.287
9NCW Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 22–334（313 aa）
Not recorded A1BW9 1-{[(6P)-3-[(3,5-dimethoxyphenyl)methyl]-6-(4-fluoro-2-methylphenyl)-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazol-8-yl]methyl}-3-methyl-1,3-dihydro-2H-imidazol-2-imine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG 3350, Bis-TRIS, HEPES, TRIS
Resolution 1.58 Å R-free 0.275
9NCW Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 22–334（313 aa）
Not recorded A1BW9 1-{[(6P)-3-[(3,5-dimethoxyphenyl)methyl]-6-(4-fluoro-2-methylphenyl)-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazol-8-yl]methyl}-3-methyl-1,3-dihydro-2H-imidazol-2-imine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG 3350, Bis-TRIS, HEPES, TRIS
Resolution 1.58 Å R-free 0.275
9NCW Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG 3350, Bis-TRIS, HEPES, TRIS
Resolution 1.58 Å R-free 0.275
9NCW Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors Deposited 2025-02-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；ammonium acetate, PEG 3350, Bis-TRIS, HEPES, TRIS
Resolution 1.58 Å R-free 0.275
9NSN Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41059 Deposited 2025-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded A1B0X N-{(1P)-5'-({(26E)-27-[(3P)-4-{[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]carbamoyl}-3-(4-chloro-2-fluorophenyl)-1H-pyrrol-2-yl]-25-oxo-3,6,9,12,15,18,21-heptaoxa-24-azaheptacos-26-en-1-yl}carbamoyl)-2'-fluoro-4-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-6-oxo-4-(trifluoromethyl)-5,6-dihydropyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.15 M cesium chloride, 15% PEG3350
Resolution 1.85 Å R-free 0.234
9NSO Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-41060 Deposited 2025-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded A1B0Y (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(34E)-1-{(1P)-6-fluoro-3'-[4-fluoro-2-(trifluoromethyl)benzamido]-4'-[(3R,5S)-3,4,5-trimethylpiperazin-1-yl][1,1'-biphenyl]-3-yl}-1,33-dioxo-5,8,11,14,17,20,23,26,29-nonaoxa-2,32-diazapentatriacont-34-en-35-yl]-1H-pyrrole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.1 M sodium citrate tribasic dihydrate, pH 4.2, 0.4 M potassium phosphate dibasic, 1.6 M sodium phosphate monobasic monohydrate
Resolution 1.85 Å R-free 0.218
9UJR Crystal structure of WDR5 in complex with peptide Ac-MRT-NH2 Deposited 2025-04-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M HEPES pH 7.0, 30% v/v Jeffamine ED-2001 pH 7.0
Resolution 2.25 Å R-free 0.235
9UJZ Crystal structure of WDR5 in complex with peptide Ac-MRTEPRP-NH2 Deposited 2025-04-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M HEPES pH 7.0, 30% v/v Jeffamine ED-2001 pH 7.0
Resolution 2.46 Å R-free 0.229
9UK1 Crystal structure of WDR5 in complex with EMBOW Deposited 2025-04-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium tartrate dibasic dihydrate, 20% w/v Polyethylene glycol 3,350, pH7.3
Resolution 2.02 Å R-free 0.226
9UK3 Crystal structure of WDR5 in complex with peptide Ac-MRTEPRPPAP-NH2 Deposited 2025-04-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.69 Å R-free 0.200
9UK4 Crystal structure of WDR5 in complex with peptide Ac-ARA-NH2 Deposited 2025-04-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M HEPES pH 7.0, 30% v/v Jeffamine ED-2001 pH 7.0
Resolution 2.12 Å R-free 0.242
9UK7 Crystal structure of WDR5 in complex with peptide Ac-MRTEP-NH2 Deposited 2025-04-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000
Resolution 1.95 Å R-free 0.237
9UK7 Crystal structure of WDR5 in complex with peptide Ac-MRTEP-NH2 Deposited 2025-04-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000
Resolution 1.95 Å R-free 0.237
9UK7 Crystal structure of WDR5 in complex with peptide Ac-MRTEP-NH2 Deposited 2025-04-17 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 22–334（313 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000
Resolution 1.95 Å R-free 0.237
9UOJ WDR5 bound with P3 Deposited 2025-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–334（314 aa）
Not recorded A1L9J ~{N}-[5-[2-fluoranyl-5-[4-[[4-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-2,1,3-benzoxadiazol-7-yl]amino]butylcarbamoyl]phenyl]-2-[(3~{R},5~{S})-3,4,5-trimethylpiperazin-1-yl]phenyl]-6-oxidanylidene-4-(trifluoromethyl)-1~{H}-pyridine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；30% (w/v) polyethylene glycol 5000, 0.2 M ammonium sulfate, and 0.1 M MES monohydrate (pH 6.5)
Resolution 1.82 Å R-free 0.254
9UXG Structure of WDR5 in complex with Peptide 2 Deposited 2025-05-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium iodide, 0.1M Bis-tris propane pH 7.5, 20% w/v PEG 3350
Resolution 1.70 Å R-free 0.243
9UXJ Structure of WDR5 in complex with Peptide 2_R4A Deposited 2025-05-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M imidazole malate (pH 7.0), and 25 % w/v PEG 4000
Resolution 1.76 Å R-free 0.225
9UXM Structure of WDR5 in complex with Peptide 1 Deposited 2025-05-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium fluoride, 0.1 M Bis-Tris propane, pH 8.5, 20% w/v PEG3350
Resolution 1.48 Å R-free 0.193
9VN5 Structure of WDR5 in complex with MBD3C R43K Deposited 2025-06-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M imidazole malate (pH 8.5) and 7.5% w/v PEG 10,000
Resolution 1.90 Å R-free 0.231
9VN5 Structure of WDR5 in complex with MBD3C R43K Deposited 2025-06-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 24–334（311 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M imidazole malate (pH 8.5) and 7.5% w/v PEG 10,000
Resolution 1.90 Å R-free 0.231
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain R 1–334（334 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLE State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain R 1–334（334 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.63 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain R 1–334（334 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain R 1–334（334 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain R 1–334（334 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å

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

View Construct and Data Evidence
UniProt name WDR5_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–313； UniProt 22–334

Histone-lysine N-methyltransferase 2A

Homo sapiens

UniProt Q03164

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–DNA Heteromer Protein × 12 DNA 2 PDB declaration: tetradecameric（14） Consistent with all polymer counts Chain C； UniProt 3762–3969 Not recorded Retinoblastoma-binding protein 5 × 1 （Q15291） WD repeat-containing protein 5 × 1 （P61964） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A × 2 （Q6AZJ8） Histone H2B 1.1 × 2 （P02281） DNA (147-MER) × 1 DNA (147-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.90 Å

Other States of the Same Protein in the Database

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

Other PDB Difference from Current Entry 6W5I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2AGH Structural basis for cooperative transcription factor binding to the CBP coactivator Deposited 2005-07-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2839–2869（31 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；298 K；Pressure 1
NMR sample composition 0.5-0.8 mM 15N,13C-labeled protein (e.g. CBP) + 3 fold excess of unlabeled binding partners (MYB + MLL), 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O | 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O
NMR sample composition 13C,15N-MYB + UNLABELED CBP & MYB, 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O | 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O
NMR sample composition 13C,15N-MLL + UNLABELED CBP & MLL, 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O | 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O
Resolution not provided
2J2S Solution structure of the nonmethyl-CpG-binding CXXC domain of the leukaemia-associated MLL histone methyltransferase Deposited 2006-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1143–1214（72 aa） Fragment：RESIDUES 1146-1214
Mutation：YES ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.5；290 K
NMR sample composition 90% WATER, 10% D2O
Resolution not provided
2JYI Solution structure of MLL CXXC domain Deposited 2007-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1147–1203（57 aa） Fragment：CXXC domain
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.1；298 K；Ionic strength (raw mmCIF value) 0.3；Pressure ambient
NMR measurement conditions pH 7.1；298 K；Ionic strength (raw mmCIF value) 0.3；Pressure ambient
NMR measurement conditions pH 7.1；298 K；Ionic strength (raw mmCIF value) 0.3；Pressure ambient
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] CXXC, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] CXXC, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] CXXC, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2KKF Solution structure of MLL CXXC domain in complex with palindromic CPG DNA Deposited 2009-06-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1147–1203（57 aa） Fragment：CXXC DOMAIN: UNP RESIDUES 1147-1203
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 25；Pressure Ambient
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] CXXC domain-1, 1 mM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-2, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] CXXC domain-3, 1 mM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-4, 100% D2O | 100% D2O
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] CXXC domain-5, 1 mM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-6, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1 mM [U-98% 15N] CXXC domain-7, 1 mM DNA (5'-D(*DCP*DCP*DCP*DTP*DGP*DCP*DGP*DCP*DAP*DGP*DGP*DG)-3')-8, 100% D2O | 100% D2O
Resolution not provided
2KU7 Solution structure of MLL1 PHD3-Cyp33 RRM chimeric protein Deposited 2010-02-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1585–1628（44 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298.2 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.3-0.5 mM [U-100% 13C; U-100% 15N] MLL PHD3-Cyp33 RRM, 20 mM sodium phosphate, 50 mM sodium chloride, 0.4 mM DSS, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
2KYU The solution structure of the PHD3 finger of MLL Deposited 2010-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1564–1628（65 aa） Fragment：PHD3 finger (UNP residues 1564-1628)
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.9；303 K
NMR sample composition 1 mM [U-98% 13C; U-98% 15N] PHD3, 100 uM ZINC ION, 25 mM potassium phosphate, 3 mM DTT, 50 mM sodium chloride, 1 mM sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2LXS Allosteric communication in the KIX domain proceeds through dynamic re-packing of the hydrophobic core Deposited 2012-08-31 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2840–2858（19 aa） Fragment：UNP RESIDUES 2840-2858
Mutation：C841A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；300 K；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_1-1, 2 mM [U-100% 13C; U-100% 15N] entity_2-2, 25 mM sodium chloride-3, 50 mM potassium phosphate-4, 1 mM sodium azide-5, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LXT Allosteric communication in the KIX domain proceeds through dynamic re-packing of the hydrophobic core Deposited 2012-08-31 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2840–2858（19 aa） Fragment：UNP RESIDUES 2840-2858
Mutation：C841A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；300 K；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] entity_1-1, 2 mM entity_2-2, 2 mM [U-100% 13C; U-100% 15N] entity_3-3, 25 mM sodium chloride-4, 50 mM potassium phosphate-5, 1 mM sodium azide-6, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MSR Solution structure of LEDGF/p75 IBD in complex with MLL1 peptide (140-160) Deposited 2014-08-05 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 140–160（21 aa） Fragment：UNP residues 140-160
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 125；Pressure ambient
NMR sample composition 0.5 mM MLL1_140, 0.5 mM [U-13C; U-15N] IBD, 25 mM HEPES, 100 mM sodium chloride, 0.05 % beta-mercaptoethanol, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2MTN Solution structure of MLL-IBD complex Deposited 2014-08-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–160（51 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 50 mM potassium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2W5Y Binary Complex of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor product S-Adenosylhomocysteine. Deposited 2008-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3785–3969（185 aa） Fragment：METHYLTRANSFERASE DOMAIN, RESIDUES 3785-3969
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；0.1 M SODIUM CACODYLATE, PH6.5, 2 % PEG 8000, 30 % 2-METHYL-2,4-PENTANDIOL, pH 6.8
Resolution 2.00 Å R-free 0.264
2W5Z Ternary Complex of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor product S-Adenosylhomocysteine and histone peptide. Deposited 2008-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 3785–3969（185 aa） Fragment：METHYLTRANSFERASE DOMAIN, RESIDUES 3785-3969
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；0.1 M SODIUM CACODYLATE PH6.8, 2 % PEG 5000, 30 % 2-METHYL-2, 4-PENTANDIOL
Resolution 2.20 Å R-free 0.247
3EG6 Structure of WDR5 bound to MLL1 peptide Deposited 2008-09-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 3762–3773（12 aa） Fragment：MLL-1 Win motif
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；298 K；30% PEG 3350, 30 mM (NH4)2SO4, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.72 Å R-free 0.240
3LQH Crystal structure of MLL1 PHD3-Bromo in the free form Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1566–1665（100 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Chain A 1703–1784（82 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.3；293 K；0.1M Sodium acetate, 50 mM NaCl, 15% PEG3350, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.72 Å R-free 0.234
3LQI Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1566–1665（100 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Chain A 1703–1784（82 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；293 K；0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.92 Å R-free 0.241
3LQI Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1566–1665（100 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Chain B 1703–1784（82 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；293 K；0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.92 Å R-free 0.241
3LQI Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1566–1665（100 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Chain C 1703–1784（82 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；293 K；0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.92 Å R-free 0.241
3LQJ Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me3 peptide Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1566–1665（100 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Chain A 1703–1784（82 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；293 K；0.1 M Tris, 0.2 M Li2SO4, 15% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.274
3LQJ Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me3 peptide Deposited 2010-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1566–1665（100 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Chain B 1703–1784（82 aa） Fragment：Third PHD finger and Bromodomain of MLL1
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；293 K；0.1 M Tris, 0.2 M Li2SO4, 15% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.274
3P4F Structural and biochemical insights into MLL1 core complex assembly and regulation. Deposited 2010-10-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 3761–3770（10 aa） Fragment：unp residues 3761-3770
Mutation：S3763A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；0.2 M ammonium citrate (buffered with hydrochloric acid/sodium hydroxide to pH 7.0) and 18% PEG3350, VAPOR DIFFUSION, HANGING DROP
Resolution 2.35 Å R-free 0.249
3U85 Crystal structure of human menin in complex with MLL1 Deposited 2011-10-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 6–25（20 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；2.3 M NaCl, pH 7.0, vapor diffusion, sitting drop, temperature 277K
Resolution 3.00 Å R-free 0.258
3U85 Crystal structure of human menin in complex with MLL1 Deposited 2011-10-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 6–25（20 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；2.3 M NaCl, pH 7.0, vapor diffusion, sitting drop, temperature 277K
Resolution 3.00 Å R-free 0.258
3U88 Crystal structure of human menin in complex with MLL1 and LEDGF Deposited 2011-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain M 103–153（51 aa）
Not recorded CHD CHOLIC ACID × 1 GGB L-CANAVANINE × 4 0BR (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLV GLYOXYLIC ACID × 4 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；277 K；1.6 M ammonium sulfate, pH 7.0, vapor diffusion, hanging drop, temperature 277K
Resolution 3.00 Å R-free 0.233
3U88 Crystal structure of human menin in complex with MLL1 and LEDGF Deposited 2011-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain N 103–153（51 aa）
Not recorded CHD CHOLIC ACID × 1 GGB L-CANAVANINE × 1 0BR (4beta,8alpha,9R)-6'-methoxy-10,11-dihydrocinchonan-9-ol × 1 GLV GLYOXYLIC ACID × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；277 K；1.6 M ammonium sulfate, pH 7.0, vapor diffusion, hanging drop, temperature 277K
Resolution 3.00 Å R-free 0.233
4ESG X-ray structure of WDR5-MLL1 Win motif peptide binary complex Deposited 2012-04-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 3755–3771（17 aa） Fragment：UNP residues 3755-3771
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.2；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.2, hanging drop, temperature 294K
Resolution 1.70 Å R-free 0.193
4ESG X-ray structure of WDR5-MLL1 Win motif peptide binary complex Deposited 2012-04-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 3755–3771（17 aa） Fragment：UNP residues 3755-3771
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 7.2；294 K；PEG3350, Ammonium Sulfate, HEPES, pH 7.2, hanging drop, temperature 294K
Resolution 1.70 Å R-free 0.193
4GQ6 Human menin in complex with MLL peptide Deposited 2012-08-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 6–15（10 aa） Fragment：unp residues 6-15
Not recorded SO4 SULFATE ION × 3 1PE PENTAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；283 K；0.2 M ammonium acetate, 0.1 M HEPES pH 7.5 and 25% w/v PEG 3,350. This solution was mixed 1:1 with 2.5mg/mL protein in 50mM Tris-HCl (pH 8.0), NBm1 peptide, 50mM NaCl, and 1mM TCEP. Prior to data collection, crystals were transferred into a cryo-solution containing 20% PEG550 MME and flash-frozen in liquid nitrogen, 1:1 molar ratio with MBM1 peptide, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 1.55 Å R-free 0.189
4NW3 Crystal structure of MLL CXXC domain in complex with a CpG DNA Deposited 2013-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1147–1204（58 aa） Fragment：CXXC zinc finger domain (UNP residues 1147-1204)
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；20% PEG3350, 0.05 M sodium tartrate, VAPOR DIFFUSION, temperature 291K
Resolution 2.82 Å R-free 0.266
5F5E The Crystal Structure of MLL1 SET domain with N3816I/Q3867L mutation Deposited 2015-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3813–3969（157 aa） Fragment：MLL1 SET domain (UNP RESIDUES 3813-3969)
Mutation：N3861I, Q3867L ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；35% Tacsimate, pH 7.0
Resolution 1.80 Å R-free 0.236
5F6L The crystal structure of MLL1 (N3861I/Q3867L) in complex with RbBP5 and Ash2L Deposited 2015-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 3813–3969（157 aa） Fragment：UNP RESIDUES 3813-3969
Mutation：N3861I, Q3867L SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；277 K；200mM NaCl, 20% PEG 3350
Resolution 1.90 Å R-free 0.213
5SVH Crystal structure of the KIX domain of CBP in complex with a MLL/c-Myb chimera Deposited 2016-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2839–2869（31 aa） Fragment：;UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315,UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315 ;
Not recorded GOL GLYCEROL × 2 CL CHLORIDE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M potassium sulfate 2.3M Ammonium sulphate
Resolution 2.05 Å R-free 0.242
5SVH Crystal structure of the KIX domain of CBP in complex with a MLL/c-Myb chimera Deposited 2016-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 2839–2869（31 aa） Fragment：;UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315,UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315 ;
Not recorded GOL GLYCEROL × 12 CL CHLORIDE ION × 42 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M potassium sulfate 2.3M Ammonium sulphate
Resolution 2.05 Å R-free 0.242
5SVH Crystal structure of the KIX domain of CBP in complex with a MLL/c-Myb chimera Deposited 2016-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2839–2869（31 aa） Fragment：;UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315,UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315 ;
Not recorded GOL GLYCEROL × 4 CL CHLORIDE ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M potassium sulfate 2.3M Ammonium sulphate
Resolution 2.05 Å R-free 0.242
6EMQ Solution structure of the LEDGF/p75 IBD - MLL1 (aa 111-160) complex Deposited 2017-10-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 110–160（51 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure arbitrary
NMR sample composition 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-MLL1, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain K 3754–3969（216 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain K 3754–3969（216 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIX Cryo-EM structure of human MLL1-NCP complex, binding mode1 Deposited 2019-07-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 3754–3969（216 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6KIZ Cryo-EM structure of human MLL1-NCP complex, binding mode2 Deposited 2019-07-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain K 3754–3969（216 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 3762–3969（208 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
6PWW Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 3762–3969（208 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 3762–3969（208 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6W5N Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Deposited 2020-03-13 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 3762–3969（208 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7MBM Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Deposited 2021-04-01 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 3762–3969（208 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.76 Å
7MBN Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Deposited 2021-04-01 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 3762–3969（208 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
7RZD CRYSTAL STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH MLL(747-755) PEPTIDE Deposited 2021-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 747–755（9 aa）
Not recorded GOL GLYCEROL × 2 CL CHLORIDE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；18-24%PEG4000, 0.1M SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
Resolution 1.82 Å R-free 0.236
7RZJ CRYSTAL STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH MLL(747-755) PHOSPHOPEPTIDE Deposited 2021-08-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 747–755（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；18-24%PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 1.80 Å R-free 0.217
7S79 STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH SYNTHETIC PHOSPHONO-MLL PEPTIDE ANALOG Deposited 2021-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 747–755（9 aa） Fragment：PHOSPHONO-MLL(747-755) PEPTIDE
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；18-24% PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
Resolution 1.53 Å R-free 0.196
7S7D STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH SYNTHETIC SULFO-MLL PEPTIDE ANALOG Deposited 2021-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 747–755（9 aa） Fragment：SULFO-MLL(747-755) PEPTIDE
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；18-24% PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
Resolution 1.56 Å R-free 0.195
7S8A STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH MLL(747-755) PHOSPHOPEPTIDE, CUBIC CRYSTAL FORM Deposited 2021-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 747–755（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 12P DODECAETHYLENE GLYCOL × 1 PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 1 PGE TRIETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 PG4 TETRAETHYLENE GLYCOL × 1 ACT ACETATE ION × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；35% PEG4000, 0.1M TRIS-HCL, PH 8.5, 0.2M SODIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
Resolution 2.10 Å R-free 0.206
7S8E STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH MLL(747-755) PHOSPHOPEPTIDE AND BOUND GLYCEROL Deposited 2021-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 747–755（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；18-24%PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
Resolution 1.60 Å R-free 0.195
7S8F STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH MLL(747-755) PEPTIDE AND BOUND GLYCEROL Deposited 2021-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 747–755（9 aa）
Not recorded GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；18-26%PEG4000, 0.1 SODIUM CITRATE, 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
Resolution 1.80 Å R-free 0.206
7U5V Crystal structure of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor product S-Adenosylhomocysteine and Borealin peptide Deposited 2022-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 3811–3969（159 aa） Fragment：SET Domain
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；60% Tacsimate pH 7.0
Resolution 2.59 Å R-free 0.304
7W67 The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 3813–3969（157 aa）
Mutation：N3861I,Q3867L,C3882SS SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.19 Å R-free 0.222
7W6A Crystal structure of the MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L complex Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 3813–3969（157 aa）
Mutation：N3861I,Q3867L,C3882SS SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5 25% w/v polyethylene glycol 3350
Resolution 2.21 Å R-free 0.229
7W6I The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me1 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 3813–3969（157 aa）
Mutation：N3861I,Q3867L,C3882SS SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3,350
Resolution 2.56 Å R-free 0.244
7W6J The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me2 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 3813–3969（157 aa）
Mutation：N3861I,Q3867L,C3882SS SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.68 Å R-free 0.252
7ZEY Complex Cyp33-RRM : MLL1-PHD3 Deposited 2022-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1564–1627（64 aa） Fragment：PHD ZINC FINGER (UNP RESIDUES 1564-1627)
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；310.15 K；Ionic strength (raw mmCIF value) 80；Pressure AMBIENT
NMR sample composition 1 mM [U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7ZEZ Trimolecular complex Cyp33-RRMdelta alpha : MLL1-PHD3 : H3K4me3 Deposited 2022-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1564–1627（64 aa） Fragment：PHD ZINC FINGER (UNP RESIDUES 1564-1627)
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；310.15 K；Ionic strength (raw mmCIF value) 80；Pressure AMBIENT
NMR sample composition 1 mM [U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 10 uM zinc chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 10 uM zinc chloride, 100% D2O | 100% D2O
NMR sample composition 1 mM PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 10 uM zinc chloride, 100% D2O | 100% D2O
Resolution not provided
9C4S Menin mutant G331R in complex with MLL peptide Deposited 2024-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 4–15（12 aa）
Mutation：C5A Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 1PE PENTAETHYLENE GLYCOL × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.54 Å R-free 0.202
9C4T menin mutant M327I in complex with MLL peptide Deposited 2024-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 4–15（12 aa）
Mutation：C5A Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 1PE PENTAETHYLENE GLYCOL × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.46 Å R-free 0.184
9C4U Menin mutant T349M in complex with MLL peptide Deposited 2024-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 4–15（12 aa）
Mutation：C5A Non-standard monomer：Yes (specific site not provided by mmCIF) PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 1PE PENTAETHYLENE GLYCOL × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.57 Å R-free 0.197
9C4V Menin mutant G331D in complex with MLL peptide Deposited 2024-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 4–15（12 aa）
Mutation：C5A Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 1PE PENTAETHYLENE GLYCOL × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；285 K；0.2 M lithium sulfate, 0.1 M HEPES, pH 7.5, 25% (w/v) PEG-3,350
Resolution 1.47 Å R-free 0.188

54 other PDB entries and 62 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KMT2A_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 2–209； UniProt 3762–3969

Set1/Ash2 histone methyltransferase complex subunit ASH2

Homo sapiens

UniProt Q9UBL3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 12 DNA 2 PDB declaration: tetradecameric（14） Consistent with all polymer counts Chain D； UniProt 2–534 Not recorded Retinoblastoma-binding protein 5 × 1 （Q15291） WD repeat-containing protein 5 × 1 （P61964） Histone-lysine N-methyltransferase 2A × 1 （Q03164） Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A × 2 （Q6AZJ8） Histone H2B 1.1 × 2 （P02281） DNA (147-MER) × 1 DNA (147-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.90 Å

Other States of the Same Protein in the Database

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

Other PDB Difference from Current Entry 6W5I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3RSN Crystal Structure of the N-terminal region of Human Ash2L Deposited 2011-05-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 96–271（176 aa） Fragment：Ash2L N-terminal domain, UNP residues 96-271
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；100 mM Tris-HCl pH8.5, 20% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.254
3S32 Crystal structure of Ash2L N-terminal domain Deposited 2011-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 95–280（186 aa） Fragment：N-terminal domain residues 95-280
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2M MgAcetate and 17-20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.45 Å R-free 0.263
3TOJ Structure of the SPRY domain of human Ash2L Deposited 2011-09-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 370–496（127 aa） Fragment：Ash2L SPRY domain, UNP residues 370-496, 539-617
Chain A 539–617（79 aa） Fragment：Ash2L SPRY domain, UNP residues 370-496, 539-617
Chain B 370–496（127 aa） Fragment：Ash2L SPRY domain, UNP residues 370-496, 539-617
Chain B 539–617（79 aa） Fragment：Ash2L SPRY domain, UNP residues 370-496, 539-617
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；20% PEG4000, 0.15 M Li2SO4, 0.1 M Tris, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.07 Å R-free 0.206
4RIQ Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30 Interacting region (SDI) Deposited 2014-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 603–618（16 aa） Fragment：UNP residues 603-618
Chain F 603–618（16 aa） Fragment：UNP residues 603-618
Chain L 603–618（16 aa） Fragment：UNP residues 603-618
Chain X 603–618（16 aa） Fragment：UNP residues 603-618
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；323 K；0.2M MgCl2, 25% PEG 3350, 0.1M Tris pH 8.5 and 10 mM spermidine, VAPOR DIFFUSION, SITTING DROP, temperature 323K
Resolution 2.23 Å R-free 0.284
4RIQ Crystal structure of DPY-30 dimerization/docking domain in complex with Ash2L Sdc1-DPY-30 Interacting region (SDI) Deposited 2014-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 603–618（16 aa） Fragment：UNP residues 603-618
Chain O 603–618（16 aa） Fragment：UNP residues 603-618
Chain R 603–618（16 aa） Fragment：UNP residues 603-618
Chain U 603–618（16 aa） Fragment：UNP residues 603-618
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；323 K；0.2M MgCl2, 25% PEG 3350, 0.1M Tris pH 8.5 and 10 mM spermidine, VAPOR DIFFUSION, SITTING DROP, temperature 323K
Resolution 2.23 Å R-free 0.284
4X8N Crystal structure of Ash2L SPRY domain in complex with phosphorylated RbBP5 Deposited 2014-12-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 380–495（116 aa） Fragment：UNP residues 380-495, 539-598
Chain A 539–598（60 aa） Fragment：UNP residues 380-495, 539-598
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol
Resolution 2.10 Å R-free 0.277
4X8P Crystal structure of Ash2L SPRY domain in complex with RbBP5 Deposited 2014-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 380–495（116 aa） Fragment：UNP residues 380-495, 539-598
Chain A 539–598（60 aa） Fragment：UNP residues 380-495, 539-598
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.2 M magnesium chloride hexahydrate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v polyethylene glycol
Resolution 2.20 Å R-free 0.271
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 380–496（117 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain A 539–598（60 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain B 380–496（117 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain B 539–598（60 aa） Fragment：UNP RESIDUES 380-496, 539-598
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 380–496（117 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain A 539–598（60 aa） Fragment：UNP RESIDUES 380-496, 539-598
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6K Crystal structure of the MLL3-Ash2L-RbBP5 complex Deposited 2015-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 380–496（117 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain B 539–598（60 aa） Fragment：UNP RESIDUES 380-496, 539-598
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；100 mM Na-Cacodylate, pH 6.5, 10% PEG 3350, 0.1 M MgCl2
Resolution 2.41 Å R-free 0.228
5F6L The crystal structure of MLL1 (N3861I/Q3867L) in complex with RbBP5 and Ash2L Deposited 2015-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 380–496（117 aa） Fragment：UNP RESIDUES 380-496, 539-598
Chain B 539–598（60 aa） Fragment：UNP RESIDUES 380-496, 539-598
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；277 K；200mM NaCl, 20% PEG 3350
Resolution 1.90 Å R-free 0.213
6E2H Crystal structure of human Ash2L (SPRY domain and SDI motif) in complex with full length DPY-30 Deposited 2018-07-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 380–622（243 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20mM citrate pH 4.7 and polyethylene glycol (PEG) 6000
Resolution 2.24 Å R-free 0.200
6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain T 95–628（534 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain T 95–628（534 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIW Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain T 95–628（534 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIX Cryo-EM structure of human MLL1-NCP complex, binding mode1 Deposited 2019-07-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain T 95–628（534 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6KIZ Cryo-EM structure of human MLL1-NCP complex, binding mode2 Deposited 2019-07-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain T 95–628（534 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain D 2–534（533 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–534（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6W5N Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Deposited 2020-03-13 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–534（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
7BRE The crystal structure of MLL2 in complex with ASH2L and RBBP5 Deposited 2020-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 286–402（117 aa） Fragment：UNP residues 286-402 and UNP residues 445-504
Chain A 445–504（60 aa） Fragment：UNP residues 286-402 and UNP residues 445-504
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Ammonium tartrate dibasic pH 7.0, 12%(w/v) Polyethylene glycol 3,350
Resolution 2.80 Å R-free 0.265
7BRE The crystal structure of MLL2 in complex with ASH2L and RBBP5 Deposited 2020-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 286–402（117 aa） Fragment：UNP residues 286-402 and UNP residues 445-504
Chain D 445–504（60 aa） Fragment：UNP residues 286-402 and UNP residues 445-504
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Ammonium tartrate dibasic pH 7.0, 12%(w/v) Polyethylene glycol 3,350
Resolution 2.80 Å R-free 0.265
7MBM Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Deposited 2021-04-01 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–534（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.76 Å
7MBN Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Deposited 2021-04-01 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–534（533 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain M 95–628（534 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
7W67 The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 380–496（117 aa）
Chain A 539–598（60 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.19 Å R-free 0.222
7W6A Crystal structure of the MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L complex Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 380–496（117 aa）
Chain A 539–598（60 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5 25% w/v polyethylene glycol 3350
Resolution 2.21 Å R-free 0.229
7W6I The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me1 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 380–496（117 aa）
Chain A 539–598（60 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3,350
Resolution 2.56 Å R-free 0.244
7W6J The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me2 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 380–496（117 aa）
Chain A 539–598（60 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.68 Å R-free 0.252
7W6L The crystal structure of MLL3-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 380–496（117 aa）
Chain A 539–598（60 aa）
Chain B 380–496（117 aa）
Chain B 539–598（60 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM sodium cacodylate, pH 6.5, 10% polyethylene glycol 3350, 0.1 M MgCl2
Resolution 2.26 Å R-free 0.223
9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain T 1–628（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.50 Å
9YLE State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric
Chain T 1–628（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.63 Å
9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric
Chain T 1–628（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.77 Å
9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain T 1–628（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.43 Å
9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric
Chain T 1–628（628 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.45 Å

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

View Construct and Data Evidence
UniProt name ASH2L_HUMAN
Isoform Q9UBL3-3
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 2–534； UniProt 2–534

Histone H3.2

Xenopus laevis

UniProt P84233

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–DNA Heteromer Protein × 12 DNA 2 PDB declaration: tetradecameric（14） Consistent with all polymer counts Chain G； UniProt 1–136 Chain K； UniProt 1–136 Not recorded Retinoblastoma-binding protein 5 × 1 （Q15291） WD repeat-containing protein 5 × 1 （P61964） Histone-lysine N-methyltransferase 2A × 1 （Q03164） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H4 × 2 （P62799） Histone H2A × 2 （Q6AZJ8） Histone H2B 1.1 × 2 （P02281） DNA (147-MER) × 1 DNA (147-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.90 Å

Other States of the Same Protein in the Database

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

Other PDB Difference from Current Entry 6W5I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1KX3 X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution Deposited 2002-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–135（135 aa）
Chain E 1–135（135 aa）
Not recorded MN MANGANESE (II) ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.275
1ZBB Structure of the 4_601_167 Tetranucleosome Deposited 2005-04-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 36-meric
Chain A 1–135（135 aa）
Chain E 1–135（135 aa）
Chain a 1–135（135 aa）
Chain e 1–135（135 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.75；294 K；magnesium chloride, potassium chloride, potassium cacodylate, trisCl, pH 6.75, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 9.00 Å
2F8N 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes Deposited 2005-12-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–135（135 aa）
Chain E 1–135（135 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；34 to 37.5mM KCl and 40-45mM MnCl2, 5mM Potassium Cacodylate, Sample concentration: 8-12 mg/ml, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.90 Å R-free 0.269
2IO5 Crystal structure of the CIA- histone H3-H4 complex Deposited 2006-10-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–135（135 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M HEPES, 0.05M cadmium sulfate hydrate, 1.0M sodium acetate tryhydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.293
3B6F Nucleosome core particle treated with cisplatin Deposited 2007-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K
Resolution 3.45 Å R-free 0.402
3B6G Nucleosome core particle treated with oxaliplatin Deposited 2007-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K
Resolution 3.45 Å R-free 0.435
3KUY DNA Stretching in the Nucleosome Facilitates Alkylation by an Intercalating Antitumor Agent Deposited 2009-11-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MN MANGANESE (II) ION × 1 ATV 2-[(2R)-oxiran-2-ylmethyl]-1H-benzo[de]isoquinoline-1,3(2H)-dione × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6；291 K；85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, EVAPORATION
Resolution 2.90 Å R-free 0.286
3KWQ Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Deposited 2009-12-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 39–136（98 aa） Fragment：UNP residues 39-136
Chain E 39–136（98 aa） Fragment：UNP residues 39-136
Mutation：K57E Mutation：K57E No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.50 Å R-free 0.315
3KXB Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Deposited 2009-12-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：K57E, G103A Mutation：K57E, G103A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；Crystals were grown by vapor diffusion in 8 20 days at 20 C using a droplet containing 4.0 mg ml−1 core particle 50 mM KCl, 70 75 mM MnCl , and 20 mM potassium cacodylate, pH 6.0, surrounded by silicon oil DC200 (110mPa s; Fluka) and equilibrated against 40 46 mM MnCl2, 35 40 mM KCl and 20 mM potassium cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 293K
Resolution 3.20 Å R-free 0.292
3LEL Structural Insight into the Sequence-Dependence of Nucleosome Positioning Deposited 2010-01-15 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 × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85mM MnCl2, 60mM KCl, 20mM K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.300
3LEL Structural Insight into the Sequence-Dependence of Nucleosome Positioning Deposited 2010-01-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded MN MANGANESE (II) ION × 19 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85mM MnCl2, 60mM KCl, 20mM K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.300
3LJA Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome Deposited 2010-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 45 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, EVAPORATION
Resolution 2.75 Å R-free 0.259
3LZ0 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 1) Deposited 2010-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K cacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.318
3LZ1 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 2) Deposited 2010-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；Kcacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.319
3MGP Binding of Cobalt ions to the Nucleosome Core Particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded CL CHLORIDE ION × 4 CO COBALT (II) ION × 43 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 2.44 Å R-free 0.282
3MGQ Binding of Nickel ions to the Nucleosome Core Particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded NI NICKEL (II) ION × 47 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 2.65 Å R-free 0.276
3MGR Binding of Rubidium ions to the Nucleosome Core Particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded CL CHLORIDE ION × 4 RB RUBIDIUM ION × 5 MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 2.30 Å R-free 0.267
3MGS Binding of Cesium ions to the Nucleosome Core particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded CL CHLORIDE ION × 4 CS CESIUM ION × 12 MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 3.15 Å R-free 0.238
3MNN A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core Deposited 2010-04-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RU RUTHENIUM ION × 3 MML 1-methyl-4-(1-methylethyl)benzene × 3 PTW 1,3,5-triaza-7-phosphatricyclo[3.3.1.1~3,7~]decane × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；55mM KCl, 85mM MnCl2, 20mM K-Cacodylate, pH 6, VAPOR DIFFUSION, temperature 291K
Resolution 2.50 Å R-free 0.277
3MVD Crystal structure of the chromatin factor RCC1 in complex with the nucleosome core particle Deposited 2010-05-04 Different construct Different oligomeric state 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 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；294 K；25 mM sodium acetate buffer, 25 mM sodium citrate, 1 mM DTT, 6 % PEG2000-MME, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 2.90 Å R-free 0.215
3O62 Nucleosome core particle modified with a cisplatin 1,3-cis-{Pt(NH3)2}2+-d(GpTpG) intrastrand cross-link Deposited 2010-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded CPT Cisplatin × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；40-46 mM MnCl2, 30-45 mM KCl, and 20 mM potassium cacodylate pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.22 Å R-free 0.306
3REH 2.5 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Deposited 2011-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；KCl, MnCl2, K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.50 Å R-free 0.270
3REI 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride Deposited 2011-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded PT PLATINUM (II) ION × 49 SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.65 Å R-free 0.276
3REJ 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Deposited 2011-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MN MANGANESE (II) ION × 13 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.55 Å R-free 0.262
3REK 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Oxaliplatin Deposited 2011-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MN MANGANESE (II) ION × 2 PT PLATINUM (II) ION × 40 SO4 SULFATE ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å R-free 0.281
3REL 2.7 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Triamminechloroplatinum(II) Chloride Deposited 2011-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MN MANGANESE (II) ION × 2 PT PLATINUM (II) ION × 48 SO4 SULFATE ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.302
3TU4 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Deposited 2011-09-15 Different construct Different oligomeric state 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 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.241
3TU4 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Deposited 2011-09-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.241
3UT9 Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601' Derivative (NCP-601L) Deposited 2011-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 29 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.20 Å R-free 0.289
3UTA Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence Containing Two TTAAA elements (NCP-TA2) Deposited 2011-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.07 Å R-free 0.266
3UTB Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite Sequence (NCP146b) Deposited 2011-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MN MANGANESE (II) ION × 21 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.20 Å R-free 0.275
4EO5 Yeast Asf1 bound to H3/H4G94P mutant Deposited 2012-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 62–136（75 aa） Fragment：residues 60-135
Mutation：G102A ACT ACETATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；298 K；7.14% PEG 3350, 0.2 M Magnesium Acetate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.35 Å R-free 0.240
4J8U X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)osmium(II) Deposited 2013-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded SO4 SULFATE ION × 3 ELJ chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)osmium(II) × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.38 Å R-free 0.280
4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain A 2–136（135 aa）
Not recorded SO4 SULFATE ION × 1 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.58 Å R-free 0.273
4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain E 2–136（135 aa）
Not recorded SO4 SULFATE ION × 2 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.58 Å R-free 0.273
4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded SO4 SULFATE ION × 3 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.58 Å R-free 0.273
4J8W X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) Deposited 2013-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded SO4 SULFATE ION × 3 1MK chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.41 Å R-free 0.275
4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain A 2–136（135 aa）
Not recorded SO4 SULFATE ION × 1 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.87 Å R-free 0.280
4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain E 2–136（135 aa）
Not recorded SO4 SULFATE ION × 2 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.87 Å R-free 0.280
4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded SO4 SULFATE ION × 3 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.87 Å R-free 0.280
4KGC Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM Deposited 2013-04-29 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 HRU (ethane-1,2-diamine-kappa~2~N,N')[(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)cyclohexane-1,2,3,4,5,6-hexayl]ruthenium × 4 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.69 Å R-free 0.282
4LD9 Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle Deposited 2013-06-24 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293.15 K；50 mM MES pH 6.5, 12% PEG 400, 12 mM MnCl2, 100 mM NaCl, 10 mM EDTA, VAPOR DIFFUSION, temperature 293.15K
Resolution 3.31 Å R-free 0.295
4R8P Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle Deposited 2014-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions Modified micro batch under oil；pH 7.5；294 K；25 mM HEPES pH 7.5, 80 mM NH4NO3, 3 % PEG2000-MME, Modified micro batch under oil, temperature 294K
Resolution 3.28 Å R-free 0.245
4WU8 Structure of trPtNAP-NCP145 Deposited 2014-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：G102A Mutation：G102A CX3 [2-(3-{bis[2-(amino-kappaN)ethyl]amino-kappaN}propyl)-1H-benzo[de]isoquinoline-1,3(2H)-dionato(2-)]platinum(1+) × 2 SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.45 Å R-free 0.263
4WU9 Structure of cisPtNAP-NCP145 Deposited 2014-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：G102A Mutation：G102A SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 CX8 [2-{3-[(2-{[2-(amino-kappaN)ethyl]amino-kappaN}ethyl)amino-kappaN]propyl}-1H-benzo[de]isoquinoline-1,3(2H)-dionato(3-)]platinum × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.60 Å R-free 0.273
4XUJ Nucleosome core particle containing adducts from treatment with a thiomorpholine-substituted [(eta-6-p-cymene)Ru(3-hydroxy-2-pyridone)Cl] compound Deposited 2015-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa） Fragment：UNP residues 2-136
Chain E 2–136（135 aa） Fragment：UNP residues 2-136
Not recorded SO4 SULFATE ION × 3 4A6 [(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)benzene]ruthenium × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40mM MnCl2, 30mM KCl, 20mM K-Cacodylate
Resolution 3.18 Å R-free 0.299
4XZQ Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-02-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 39–136（98 aa） Fragment：residues 39-136
Chain E 39–136（98 aa） Fragment：residues 39-136
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292.15 K；potassium chloride, potassium cacodylate, manganese chloride
Resolution 2.40 Å R-free 0.299
4YS3 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-03-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 39–136（98 aa） Fragment：residues 39-136
Chain E 39–136（98 aa） Fragment：residues 39-136
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；292.15 K；postassium chloride, manganese chloride, cacodylate
Resolution 3.00 Å R-free 0.279
4Z66 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-04-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 39–136（98 aa）
Chain E 39–136（98 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292.15 K；potassium chloride, potassium cacodylate, manganese chloride
Resolution 2.50 Å R-free 0.296
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
Resolution 3.82 Å R-free 0.256
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
Resolution 3.82 Å R-free 0.256
5BS7 Structure of histone H3/H4 in complex with Spt2 Deposited 2015-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 26–136（111 aa） Fragment：residues 26-136
Chain B 26–136（111 aa） Fragment：residues 26-136
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；0.02 M NaCl, 0.2 M HEPES 7.5, 1.5 M ammonium sulfate
Resolution 3.30 Å R-free 0.290
5BSA Structure of histone H3/H4 in complex with Spt2 Deposited 2015-06-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 27–136（110 aa） Fragment：residues 27-136
Chain B 27–136（110 aa） Fragment：residues 27-136
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；0.02 M NaCl, 0.2 M HEPES 7.5, 1.6 M ammonium sulfate
Resolution 4.61 Å R-free 0.329
5CP6 Nucleosome Core Particle with Adducts from the Anticancer Compound, [(eta6-5,8,9,10-tetrahydroanthracene)Ru(ethylenediamine)Cl][PF6] Deposited 2015-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded RUH (ethane6-5,8,9,10-tetrahydroanthracene)Ru(II)(ethylene-diamine)Cl × 3 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.251
5DNM Nucleosome core particle containing adducts of ruthenium(II)-toluene PTA complex Deposited 2015-09-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RAX dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate
Resolution 2.81 Å R-free 0.241
5DNN Nucleosome core particle containing adducts of gold(I)-triethylphosphane and ruthenium(II)-toluene PTA complexes Deposited 2015-09-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded AUF triethylphosphanuidylgold(1+) × 2 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RAX dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate
Resolution 2.80 Å R-free 0.236
5E5A Crystal structure of the chromatin-tethering domain of Human cytomegalovirus IE1 protein bound to the nucleosome core particle Deposited 2015-10-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；289 K；sodium cacodylate, magnesium acetate, 2-methyl-2,4-pentanediol
Resolution 2.81 Å R-free 0.242
5F99 X-ray Structure of the MMTV-A Nucleosome Core Particle Deposited 2015-12-09 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 × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：C110A Mutation：C110A CL CHLORIDE ION × 4 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；sample was mixed 1:1 with 10 mM K-cacodylate, pH 6.0, 180 mM MgCl2, 50 mM KCl and equilibrated against a 1:4 dilution of the same solution
Resolution 2.63 Å R-free 0.252
5HQ2 Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle Deposited 2016-01-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: hexadecameric
Chain A 2–136（135 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 5.5；277 K；25 mM sodium acetate pH 5.5, 40 mM sodium citrate,1 mM DTT, 6% PEG2000-MME
Resolution 4.50 Å R-free 0.397
5KGF Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution Deposited 2016-06-13 Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；High concentration NCP-ubme/GST-53BP1 complex at 200 mM salt was diluted just prior to grid freezing.
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Plunged into liquid ethane-propane (FEI VITROBOT MARK III)
Resolution 4.54 Å
5MLU Crystal structure of the PFV GAG CBS bound to a mononucleosome Deposited 2016-12-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 40–136（97 aa）
Chain E 40–136（97 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.05M MnCl2, 0.04M KCl, 0.1M potassium cacodylate pH 6.0, 5% trehalose, 24% MPD
Resolution 2.80 Å R-free 0.252
5NL0 Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1 Deposited 2017-04-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293.15 K；Mix of equal volumes of the nucleosome/H1 complex (25-30 microM) and a crystallization solution composed of MPD (6% v/v), 50 mM NaCl, and 50 mM sodium potassium phosphate pH 6.4.
Resolution 5.40 Å R-free 0.265
5NL0 Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1 Deposited 2017-04-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain K 2–136（135 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293.15 K；Mix of equal volumes of the nucleosome/H1 complex (25-30 microM) and a crystallization solution composed of MPD (6% v/v), 50 mM NaCl, and 50 mM sodium potassium phosphate pH 6.4.
Resolution 5.40 Å R-free 0.265
5O9G Structure of nucleosome-Chd1 complex Deposited 2017-06-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
5OMX X-ray Structure of the H2A-N38C Nucleosome Core Particle Deposited 2017-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：C110A Mutation：C110A MN MANGANESE (II) ION × 33 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；8 mg/ml sample was mixed 1:1 with 10 mM K-Cacodylate (pH 6.0), 140-150 mM MnCl2, 100 KCl. and equilibrated against a 1:4 dilution of the same solution
Resolution 2.32 Å R-free 0.259
5ONG X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer Deposited 2017-08-03 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 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：C110A, R40C Mutation：C110A, R40C MN MANGANESE (II) ION × 20 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；Sample was mixed in a 1:1 ratio with 10 mM Na-cacodylate, pH 6.0, 130-180 mM MnCl2, 100-160 mM KCl and equilibrated against a 1:4 dilution of the same solution
Resolution 2.80 Å R-free 0.247
5ONW X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two H2A/H2B dimers crosslinked via H2A N38C Deposited 2017-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：C110A, R40C Mutation：C110A, R40C MN MANGANESE (II) ION × 20 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；Sample was mixed in a 1:1 ratio with 10 mM Na-cacodylate, pH 6.0, 160-210 mM MnCl2, 140-200 mM KCl and equilibrated against a 1:4 dilution of the same solution
Resolution 2.80 Å R-free 0.254
5OXV Structure of the 4_601_157 tetranucleosome (C2 form) Deposited 2017-09-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain K 2–136（135 aa）
Chain O 2–136（135 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；30-60 mM KCl, 90-110 mM MgCl2 and 5 mM Na-cacodylate, pH 6
Resolution 6.72 Å R-free 0.352
5X0X Complex of Snf2-Nucleosome complex with Snf2 bound to position +6 of the nucleosome Deposited 2017-01-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
5X0Y Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome Deposited 2017-01-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.69 Å
5XF6 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 EDN ETHANE-1,2-DIAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0
Resolution 2.63 Å R-free 0.254
5Z3L Structure of Snf2-nucleosome complex in apo state Deposited 2018-01-08 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.31 Å
5Z3O Structure of Snf2-nucleosome complex in ADP state Deposited 2018-01-08 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
5Z3U Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state Deposited 2018-01-08 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.31 Å
5Z3V Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state Deposited 2018-01-08 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.22 Å
6ESF Nucleosome : Class 1 Deposited 2017-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ESG Nucleosome breathing : Class 2 Deposited 2017-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.40 Å
6ESH Nucleosome breathing : Class 3 Deposited 2017-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
6ESI Nucleosome breathing : Class 4 Deposited 2017-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
6I84 Structure of transcribing RNA polymerase II-nucleosome complex Deposited 2018-11-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain M 1–136（136 aa）
Chain S 1–136（136 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6JM9 cryo-EM structure of DOT1L bound to unmodified nucleosome Deposited 2019-03-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 39–136（98 aa）
Chain E 39–136（98 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.30 Å
6JMA cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome Deposited 2019-03-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 39–136（98 aa）
Chain E 39–136（98 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6KW3 The ClassA RSC-Nucleosome Complex Deposited 2019-09-05 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain N 1–136（136 aa）
Chain Q 1–136（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.13 Å
6KW4 The ClassB RSC-Nucleosome Complex Deposited 2019-09-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain N 1–136（136 aa）
Chain Q 1–136（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.55 Å
6KW5 The ClassC RSC-Nucleosome Complex Deposited 2019-09-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain R 1–136（136 aa）
Chain V 1–136（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 10.13 Å
6NE3 Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at SHL-2 Deposited 2018-12-16 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G102A Mutation：G102A ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；2.5 ul of nucleosome-443 SNF2h complexes were applied to a glow discharged Quantifoil holey carbon grid (1.2 um hole size, 400 mesh), blotted in a Vitrobot Mark I (FEI Company) using 6 seconds blotting at 100% humidity, and then plunge-frozen in liquid ethane cooled by liquid nitrogen.
Resolution 3.90 Å
6NJ9 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex Deposited 2019-01-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：G102A, K79Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：G102A, K79Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) SAM S-ADENOSYLMETHIONINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing.
Resolution 2.96 Å
6NN6 Structure of Dot1L-H2BK120ub nucleosome complex Deposited 2019-01-14 Different construct Different mutation/modification Different oligomeric state 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）
Mutation：G103A Mutation：G103A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6NOG Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome Deposited 2019-01-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：G102A Mutation：G102A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing
Resolution 3.90 Å
6NQA Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex Deposited 2019-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：G102A, K79Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：G102A, K79Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing.
Resolution 3.54 Å
6O22 Structure of Asf1-H3:H4-Rtt109-Vps75 histone chaperone-lysine acetyltransferase complex with the histone substrate. Deposited 2019-02-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule Experimental method not declared
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition 70 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 70 uM Rtt109, 70 uM Asf1, 70 uM H3, 70 uM H4, 100% D2O | 100% D2O
NMR sample composition 70 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 70 uM Rtt109, 70 uM Asf1, 70 uM H3(110A,63C) mutant with a cysteine coupled to a paramagnetic tag, 70 uM H4, 100% D2O | 100% D2O
NMR sample composition 90 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 90 uM Rtt109, 90 uM Asf1, 90 uM H3(110A,76C) mutant with a cysteine coupled to a paramagnetic tag, 90 uM H4, 100% D2O | 100% D2O
NMR sample composition 30 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 30 uM Rtt109, 30 uM Asf1, 30 uM H3, 30 uM H4(30C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2O | 100% D2O
NMR sample composition 70 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 70 uM Rtt109, 70 uM Asf1, 70 uM H3, 70 uM H4(82C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2O | 100% D2O
NMR sample composition 80 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 80 uM Rtt109, 80 uM Asf1, 80 uM H3, 80 uM H4(45C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2O | 100% D2O
NMR sample composition 30 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 30 uM Rtt109, 30 uM Asf1, 30 uM H3, 30 uM H4(93C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2O | 100% D2O
Resolution not provided
6O96 Dot1L bound to the H2BK120 Ubiquitinated nucleosome Deposited 2019-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：G102A Mutation：G102A SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen PROPANE；blotted for 3s before plunging
Resolution 3.50 Å
6OM3 Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle Deposited 2019-04-18 Different construct Different mutation/modification Different oligomeric state 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）
Mutation：G102A Mutation：G102A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277.15 K；6 mM Na-Cacodylate pH 6.0, 0.4 mM Spermine-HCl, 2 mM MgCl2 and 1.75% v/v PEG 400
Resolution 3.30 Å R-free 0.250
6OM3 Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle Deposited 2019-04-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain M 2–136（135 aa）
Chain Q 2–136（135 aa）
Mutation：G102A Mutation：G102A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277.15 K；6 mM Na-Cacodylate pH 6.0, 0.4 mM Spermine-HCl, 2 mM MgCl2 and 1.75% v/v PEG 400
Resolution 3.30 Å R-free 0.250
6PA7 The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. Deposited 2019-06-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded CL CHLORIDE ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain G 1–136（136 aa）
Chain K 1–136（136 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
6PWW Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain G 1–136（136 aa）
Chain K 1–136（136 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6PWX Cryo-EM structure of RbBP5 bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain G 1–136（136 aa）
Chain K 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6R1U Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2 Deposited 2019-03-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.36 Å
6RYR Nucleosome-CHD4 complex structure (single CHD4 copy) Deposited 2019-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6RYU Nucleosome-CHD4 complex structure (two CHD4 copies) Deposited 2019-06-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6T9L SAGA DUB module bound to a ubiqitinated nucleosome Deposited 2019-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.60 Å
6TDA Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome Deposited 2019-11-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.00 Å
6UXW SWI/SNF nucleosome complex with ADP-BeFx Deposited 2019-11-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain R 2–136（135 aa）
Chain V 2–136（135 aa）
Not recorded PO4 PHOSPHATE ION × 12 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM HEPES, pH 7.9, 10 mM MgCl2, 50 mM KCl, 1 mM DTT, 5% glycerol, 0.05% NP-40
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.96 Å
6VEN Yeast COMPASS in complex with a ubiquitinated nucleosome Deposited 2020-01-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：K4(NLE), M90(NLE), M120(NLE), G102A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K4(NLE), M90(NLE), M120(NLE), G102A Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 5 3.5 sec blot time
Resolution 3.37 Å
6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain G 1–136（136 aa）
Chain K 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6W5N Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Deposited 2020-03-13 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain G 1–136（136 aa）
Chain K 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
6WKR PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome Deposited 2020-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: octadecameric
Chain I 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6WZ5 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-13 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
6WZ9 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-13 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6X0N Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-16 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 23-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Chain a 2–136（135 aa）
Chain e 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 10.00 Å
6Z6P HDAC-PC-Nuc Deposited 2020-05-28 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain E 40–136（97 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.43 Å
7AT8 Histone H3 recognition by nucleosome-bound PRC2 subunit EZH2. Deposited 2020-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 2–136（135 aa）
Chain H 2–136（135 aa）
Not recorded ZN ZINC ION × 7 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.40 Å
7EG6 Snf5 Finger Helix bound to the nucleosome Deposited 2021-03-24 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7EGP The structure of SWI/SNF-nucleosome complex Deposited 2021-03-24 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain O 2–136（135 aa）
Chain S 2–136（135 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
7ENN The structure of ALC1 bound to the nucleosome Deposited 2021-04-18 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7K6P Active state Dot1 bound to the unacetylated H4 nucleosome Deposited 2020-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 38–135（98 aa）
Chain E 38–135（98 aa）
Mutation：K79M, G103A Mutation：K79M, G103A SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7K6Q Active state Dot1 bound to the H4K16ac nucleosome Deposited 2020-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 38–135（98 aa）
Chain E 38–135（98 aa）
Mutation：K79M, G103A Mutation：K79M, G103A SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7KBD Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction) Deposited 2020-10-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
7KBE Nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction) Deposited 2020-10-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7KBF H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction) Deposited 2020-10-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.42 Å
7NKX RNA polymerase II-Spt4/5-nucleosome-Chd1 structure Deposited 2021-02-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7NKY RNA Polymerase II-Spt4/5-nucleosome-FACT structure Deposited 2021-02-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 24 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 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7OH9 Nucleosome with TBP and TFIIA bound at SHL -6 Deposited 2021-05-09 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7OHA nucleosome with TBP and TFIIA bound at SHL +2 Deposited 2021-05-09 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7OHB TBP-nucleosome complex Deposited 2021-05-10 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHC Cryo-EM structure of nucleosome core particle composed of the Widom 601 DNA sequence Deposited 2021-05-10 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7OTQ Cryo-EM structure of ALC1/CHD1L bound to a PARylated nucleosome Deposited 2021-06-10 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：C110A Mutation：C110A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 uL were applied on grid and immediately blotted for 2.5 s at blot force 0.
Resolution 4.80 Å
7SSA Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome Deposited 2021-11-10 Different construct Different oligomeric state 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 No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7UNC Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome Deposited 2022-04-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 29 PDB declaration: 32-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Mutation：G102A Mutation：G102A ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7UND Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) Deposited 2022-04-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Mutation：G102A Mutation：G102A ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7XFC Structure of nucleosome-DI complex (-30I, Apo state) Deposited 2022-04-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.90 Å
7XFH Structure of nucleosome-AAG complex (A-30I, post-catalytic state) Deposited 2022-04-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.90 Å
7XFI Structure of nucleosome-DI complex (-50I, Apo state) Deposited 2022-04-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.90 Å
7XFJ Structure of nucleosome-AAG complex (T-50I, post-catalytic state) Deposited 2022-04-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.00 Å
7XFL Structure of nucleosome-AAG complex (A-53I, free state) Deposited 2022-04-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.80 Å
7XFM Structure of nucleosome-AAG complex (A-53I, post-catalytic state) Deposited 2022-04-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.10 Å
7XFN Structure of nucleosome-DI complex (-55I, Apo state) Deposited 2022-04-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.80 Å
7XNP Structure of nucleosome-AAG complex (A-55I, post-catalytic state) Deposited 2022-04-29 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.90 Å
7YRD histone methyltransferase Deposited 2022-08-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 34–136（103 aa）
Chain E 34–136（103 aa）
Mutation：G2E,G70A Mutation：G2E,G70A ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7YRG histone methyltransferase Deposited 2022-08-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 34–136（103 aa）
Chain E 34–136（103 aa）
Mutation：G2E,G70A Mutation：G2E,G70A ZN ZINC ION × 2 SAM S-ADENOSYLMETHIONINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain a 2–136（135 aa）
Chain e 2–136（135 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain a 2–136（135 aa）
Chain e 2–136（135 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain a 2–136（135 aa）
Chain e 2–136（135 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
8A3Y Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex Deposited 2022-06-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information 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 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Mutation：G103A Mutation：G103A SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Mutation：G103A Mutation：G103A SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8BZ1 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Deposited 2022-12-14 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Mutation：G103A Mutation：G103A ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8CEO Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Deposited 2023-02-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain r 2–136（135 aa）
Chain v 2–136（135 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8F86 SIRT6 bound to an H3K9Ac nucleosome Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZSL [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3aR,5R,6R,6aR)-6-hydroxytetrahydro-2H-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8G6Q H2AK119ub-modified nucleosome ubiquitin position 1 Deposited 2023-02-15 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G102A Mutation：G102A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.41 Å
8G6S H2AK119ub-modified nucleosome ubiquitin position 2 Deposited 2023-02-15 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G102A Mutation：G102A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
8G86 Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of nucleosome) Deposited 2023-02-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
8G88 Human Oct4 bound to nucleosome with human nMatn1 sequence Deposited 2023-02-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
8G8B Nucleosome with human nMatn1 sequence in complex with Human Oct4 Deposited 2023-02-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
8G8G Interaction of H3 tail in LIN28B nucleosome with Oct4 Deposited 2023-02-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8GPN Human menin in complex with H3K79Me2 nucleosome Deposited 2022-08-26 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：K79 dimethylation Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K79 dimethylation Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8OF4 Nucleosome Bound human SIRT6 (Composite) Deposited 2023-03-13 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
8RUP Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome Deposited 2024-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain A 1–136（136 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；3 s blotting time, -10 force, no wait time.
Resolution 2.42 Å
8RUQ Borealin N-terminus in complex with H3.T3p-nucleosome Deposited 2024-01-31 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；3 s blotting time, -10 force, no wait time.
Resolution 2.29 Å
8SIY Origin Recognition Complex Associated (ORCA) protein bound to H4K20me3-nucleosome Deposited 2023-04-17 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–136（135 aa）
Chain G 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8SKZ Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome Deposited 2023-04-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8SVF BAP1/ASXL1 bound to the H2AK119Ub Nucleosome Deposited 2023-05-16 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G103A Mutation：G103A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8T3T Structure of Bre1-nucleosome complex - state3 Deposited 2023-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.21 Å
8T3W Structure of Bre1-nucleosome complex - state2 Deposited 2023-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
8T3Y Structure of Bre1-nucleosome complex - state1 Deposited 2023-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES, pH 7.5, 50 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
8T9F Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Deposited 2023-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8T9G Automethylated PRC2 dimer bound to nucleosome Deposited 2023-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain A 1–136（136 aa）
Chain W 1–136（136 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
8T9H Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Deposited 2023-06-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
8TAS PRC2 monomer bound to nucleosome Deposited 2023-06-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain I 1–136（136 aa）
Chain W 1–136（136 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8TB9 PRC2-J119-450 monomer bound to H1-nucleosome Deposited 2023-06-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain I 1–136（136 aa）
Chain W 1–136（136 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8THU Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Deposited 2023-07-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8UW1 Cryo-EM structure of DNMT3A1 UDR in complex with H2AK119Ub-nucleosome Deposited 2023-11-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8UXQ Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome Deposited 2023-11-09 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain E 2–136（135 aa）
Chain K 2–136（135 aa）
Mutation：C110A Mutation：C110A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
8V25 H2BK120ub-modified nucleosome ubiquitin position 1 Deposited 2023-11-21 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G102A Mutation：G102A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
8V26 H2BK120ub-modified nucleosome ubiquitin position 2 Deposited 2023-11-21 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G102A Mutation：G102A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
8V27 H2BK120ub-modified nucleosome ubiquitin position 3 Deposited 2023-11-21 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G102A Mutation：G102A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
8V28 H2BK120ub-modified nucleosome ubiquitin position 4 Deposited 2023-11-22 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G102A Mutation：G102A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
8V4Y Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 1) Deposited 2023-11-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：G102A, C110A Mutation：G102A, C110A ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8V6V Cryo-EM structure of doubly-bound SNF2h-nucleosome complex Deposited 2023-12-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：G102A, C110A Mutation：G102A, C110A ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8V7L Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 2) Deposited 2023-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：G102A, C110A Mutation：G102A, C110A ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8VX5 Nucleosome core particle containing an 8-oxoG damage site Deposited 2024-02-03 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G102A Mutation：G102A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8VX6 Human OGG1 bound at the nucleosomal DNA entry site Deposited 2024-02-03 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G102A Mutation：G102A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9B2S Haspin bound to nucleosome in position 1 Deposited 2024-03-16 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G102A Mutation：G102A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
9B2T Haspin bound to nucleosome in position 2 Deposited 2024-03-16 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G102A Mutation：G102A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å
9B2U Haspin bound to H3 tail Deposited 2024-03-16 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–136（136 aa）
Mutation：G102A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.64 Å
9CA7 Cryo-EM structure of human SRCAP-nucleosome complex in the fully-engaged state (composite structure) Deposited 2024-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain U 2–136（135 aa）
Chain W 2–136（135 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 5 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
9CA8 Cryo-EM structure of human SRCAP-nucleosome complex in the partially-engaged state (composite structure) Deposited 2024-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain U 2–136（135 aa）
Chain W 2–136（135 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 5 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
9CAA Cryo-EM structure of human SRCAP-nucleosome complex in the pre-engaged state (composite structure) Deposited 2024-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain U 2–136（135 aa）
Chain W 2–136（135 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.04 Å
9CAB Cryo-EM structure of human SRCAP-nucleosome complex in the encounter state (composite structure) Deposited 2024-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain U 2–136（135 aa）
Chain W 2–136（135 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 5 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.94 Å
9CG9 Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2 Deposited 2024-06-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Mutation：G102A, C110A Mutation：G102A, C110A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 uL of sample was applied to grid.
Resolution 2.94 Å
9DBY ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome Deposited 2024-08-24 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G103A Mutation：G103A ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9DDE ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome Deposited 2024-08-28 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G103A Mutation：G103A ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9DG3 ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome Deposited 2024-09-01 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G103A Mutation：G103A ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9DGG ncPRC1RYBP bound to unmodified nucleosome Deposited 2024-09-02 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Mutation：G103A Mutation：G103A ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9E1L Snf2h bound nucleosome complex - ClassA1 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
9E1M Snf2h bound nucleosome complex - ClassA2 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
9E1N Snf2h bound nucleosome complex-ClassA3 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9E1O Snf2h bound nucleosome complex - ClassB1 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E1P Snf2h bound nucleosome complex - ClassB2 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
9E1Q Snf2h bound nucleosome complex - ClassB3 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9E1R Snf2h bound nucleosome complex - ClassB4 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9E1U Snf2h bound nucleosome complex - ClassC1 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9E1V Snf2h bound nucleosome complex - ClassC2 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9E1W Snf2h bound nucleosome complex - ClassC3 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9E1X Snf2h bound nucleosome complex - ClassD1 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9E1Y Empty Nucleosome with 601 widom sequence Deposited 2024-10-21 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EIL SIRT6 bound to an H3K27Ac nucleosome Deposited 2024-11-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZSL [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3aR,5R,6R,6aR)-6-hydroxytetrahydro-2H-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9F0O The molecular basis and modulation of lamin-specific chromatin interaction Deposited 2024-04-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 39–136（98 aa）
Chain E 39–136（98 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9GD0 Structure of a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9GD1 Structure of Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9GD2 Structure of Chd1 bound to a dinucleosome with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9GD3 Structure of a mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA. Deposited 2024-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9GEN Recombinant Myeloperoxidase bound to nucleosome core particle Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.76 Å
9GEO Nucleosome core particle Deposited 2024-08-07 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.79 Å
9GEP Native monomeric Myeloperoxidase bound to nucleosome core particle Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
9GEQ Native dimeric Myeloperoxidase bound to nucleosome core particle; composite map Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded CL CHLORIDE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9GER Native dimeric Myeloperoxidase bound to nucleosome core particle, intermediate state; composite map Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded CL CHLORIDE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.58 Å
9IHD Nucleosome core particle bound by one molecule of DTT-reduced native monomeric myeloperoxidase Deposited 2025-02-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
9IHE Nucleosome core particle bound by two molecules of DTT-reduced native monomeric myeloperoxidase Deposited 2025-02-21 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9IHF Nucleosome core particle bound by one monomer and one dimer of of DTT-reduced native myeloperoxidase Deposited 2025-02-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain A 38–136（99 aa）
Chain E 38–136（99 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9MPP The cryo-EM structure of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L Deposited 2024-12-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded ZN ZINC ION × 6 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9N6K 2.88 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex with DNA-binding domain Deposited 2025-02-05 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 40–136（97 aa）
Chain E 40–136（97 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9NH8 CHD1-nucleosome complex (anchored state) Deposited 2025-02-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain V 1–136（136 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ARG ARGININE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9NY4 USP21 bound to H2AK119ub nucleosome Deposited 2025-03-26 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9QAJ Structure of the nucleosome-bound human BCL7A Deposited 2025-02-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9R5K Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-09 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Hepes, 120mM Nacl
cryo-EM vitrification conditions Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity
Resolution 4.20 Å
9R5S Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-09 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Hepes, 120mM Nacl
cryo-EM vitrification conditions Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity
Resolution 3.80 Å
9R5W Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-10 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Hepes, 120mM Nacl
cryo-EM vitrification conditions Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity
Resolution 3.80 Å
9SI3 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome Deposited 2025-08-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
9SI9 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class0) Deposited 2025-08-28 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
9SJ5 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class1) Deposited 2025-08-29 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
9SLJ Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Double Occupancy) Deposited 2025-09-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9T4V ALC1/CHD1L in an intermediate conformation, bound to a PARylated nucleosome Deposited 2025-11-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 uL were applied on grid and immediately blotted for 2.5 s at blot force 0.
Resolution 6.60 Å
9W74 Cryo-EM structure of the close-packed di-hexasome (CPDH) Deposited 2025-08-05 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Chain K 1–136（136 aa）
Chain O 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.94 Å
9WBZ The structure of NCP-motor-ARP module of ncBAF-nucleosome complex Deposited 2025-08-15 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
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 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9WC0 The structure of NCP-RA module of ncBAF-nucleosome complex Deposited 2025-08-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
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 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
9XYC Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome LEDGF+nucleosome map Q Deposited 2025-08-25 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain a 1–136（136 aa）
Chain e 1–136（136 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9Y4P Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker Deposited 2025-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain E 2–136（135 aa）
Chain Q 2–136（135 aa）
Chain W 2–136（135 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.84 Å

230 other PDB entries and 239 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H32_XENLA
Isoform —
PDB entities 5
Chains and sequence ranges Author chain G； PDBConstruct 1–136； UniProt 1–136 Author chain K； PDBConstruct 1–136； UniProt 1–136

Histone H4

Xenopus laevis

UniProt P62799

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–DNA Heteromer Protein × 12 DNA 2 PDB declaration: tetradecameric（14） Consistent with all polymer counts Chain H； UniProt 1–103 Chain L； UniProt 1–103 Not recorded Retinoblastoma-binding protein 5 × 1 （Q15291） WD repeat-containing protein 5 × 1 （P61964） Histone-lysine N-methyltransferase 2A × 1 （Q03164） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H3.2 × 2 （P84233） Histone H2A × 2 （Q6AZJ8） Histone H2B 1.1 × 2 （P02281） DNA (147-MER) × 1 DNA (147-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.90 Å

Other States of the Same Protein in the Database

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

Other PDB Difference from Current Entry 6W5I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AOI COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) AND 146 BP LONG DNA FRAGMENT Deposited 1997-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 17–103（87 aa） Fragment：HISTONE H4
Chain F 17–103（87 aa） Fragment：HISTONE H4
Not recorded MN MANGANESE (II) ION × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å R-free 0.302
1KX3 X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution Deposited 2002-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded MN MANGANESE (II) ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.275
1P34 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.70 Å R-free 0.270
1P3A Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.00 Å R-free 0.260
1P3B Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.00 Å R-free 0.286
1P3F Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.90 Å R-free 0.272
1P3G Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.70 Å R-free 0.265
1P3I Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.30 Å R-free 0.275
1P3K Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.90 Å R-free 0.291
1P3L Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.40 Å R-free 0.265
1P3M Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.90 Å R-free 0.270
1P3O Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.75 Å R-free 0.276
1P3P Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.70 Å R-free 0.268
1ZBB Structure of the 4_601_167 Tetranucleosome Deposited 2005-04-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 36-meric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Chain b 1–102（102 aa）
Chain f 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.75；294 K；magnesium chloride, potassium chloride, potassium cacodylate, trisCl, pH 6.75, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 9.00 Å
1ZLA X-ray Structure of a Kaposi's sarcoma herpesvirus LANA peptide bound to the nucleosomal core Deposited 2005-05-05 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；Manganese chloride, Potassium chloride, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.90 Å R-free 0.277
21VV Cryo-EM structure of ncBAF bound to the nucleosome Deposited 2025-12-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 100 mM KCl, 2 mM MgCl2, 2 mM DTT, 0.5 mM ADP, 8 mM NaF, 1 mM BeSO4.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
21WA Cryo-EM structure of the ATPase domain of SMARCA4 bound to a nucleosome Deposited 2025-12-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 100 mM KCl, 2 mM MgCl2, 2 mM DTT, 0.5 mM ADP, 8 mM NaF, 1 mM BeSO4.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
21WC Cryo-EM structure of the ATPase domain of SMARCA4 and the finger helix of BCL7A bound to a nucleosome Deposited 2025-12-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 100 mM KCl, 2 mM MgCl2, 2 mM DTT, 0.5 mM ADP, 8 mM NaF, 1 mM BeSO4.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
2F8N 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes Deposited 2005-12-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；34 to 37.5mM KCl and 40-45mM MnCl2, 5mM Potassium Cacodylate, Sample concentration: 8-12 mg/ml, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.90 Å R-free 0.269
2FJ7 Crystal structure of Nucleosome Core Particle Containing a Poly (dA.dT) Sequence Element Deposited 2005-12-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；20 to 35 mM KCl, 34 to 48 mM MnCl2, and 5mM K-cacodylate pH 6.0 , VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.20 Å R-free 0.350
2HUE Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4 Deposited 2006-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 20–102（83 aa） Fragment：residues 20-102
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1M potassium sulfate, 0.1M Tris-HCl, 14.5% PEG 4K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.70 Å R-free 0.239
2HUE Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4 Deposited 2006-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 20–102（83 aa） Fragment：residues 20-102
Not recorded ZN ZINC ION × 2 GOL GLYCEROL × 4 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1M potassium sulfate, 0.1M Tris-HCl, 14.5% PEG 4K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.70 Å R-free 0.239
2HUE Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4 Deposited 2006-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 20–102（83 aa） Fragment：residues 20-102
Not recorded ZN ZINC ION × 2 GOL GLYCEROL × 4 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1M potassium sulfate, 0.1M Tris-HCl, 14.5% PEG 4K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.70 Å R-free 0.239
2HUE Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4 Deposited 2006-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 20–102（83 aa） Fragment：residues 20-102
Not recorded ZN ZINC ION × 2 GOL GLYCEROL × 4 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1M potassium sulfate, 0.1M Tris-HCl, 14.5% PEG 4K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.70 Å R-free 0.239
2IO5 Crystal structure of the CIA- histone H3-H4 complex Deposited 2006-10-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M HEPES, 0.05M cadmium sulfate hydrate, 1.0M sodium acetate tryhydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.293
2NZD Nucleosome core particle containing 145 bp of DNA Deposited 2006-11-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.65 Å R-free 0.283
3B6F Nucleosome core particle treated with cisplatin Deposited 2007-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K
Resolution 3.45 Å R-free 0.402
3B6G Nucleosome core particle treated with oxaliplatin Deposited 2007-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K
Resolution 3.45 Å R-free 0.435
3C1B The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure Deposited 2008-01-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；Manganese chloride, Potassium chloride, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.20 Å R-free 0.270
3C1C The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure Deposited 2008-01-22 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；Manganese chloride, Potassium chloride, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.15 Å R-free 0.290
3KUY DNA Stretching in the Nucleosome Facilitates Alkylation by an Intercalating Antitumor Agent Deposited 2009-11-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 1 ATV 2-[(2R)-oxiran-2-ylmethyl]-1H-benzo[de]isoquinoline-1,3(2H)-dione × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6；291 K；85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, EVAPORATION
Resolution 2.90 Å R-free 0.286
3KWQ Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Deposited 2009-12-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 21–103（83 aa） Fragment：UNP residues 21-103
Chain F 21–103（83 aa） Fragment：UNP residues 21-103
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.50 Å R-free 0.315
3KXB Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Deposited 2009-12-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；Crystals were grown by vapor diffusion in 8 20 days at 20 C using a droplet containing 4.0 mg ml−1 core particle 50 mM KCl, 70 75 mM MnCl , and 20 mM potassium cacodylate, pH 6.0, surrounded by silicon oil DC200 (110mPa s; Fluka) and equilibrated against 40 46 mM MnCl2, 35 40 mM KCl and 20 mM potassium cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 293K
Resolution 3.20 Å R-free 0.292
3LEL Structural Insight into the Sequence-Dependence of Nucleosome Positioning Deposited 2010-01-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85mM MnCl2, 60mM KCl, 20mM K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.300
3LEL Structural Insight into the Sequence-Dependence of Nucleosome Positioning Deposited 2010-01-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 2–103（102 aa）
Chain P 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 19 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85mM MnCl2, 60mM KCl, 20mM K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.300
3LJA Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome Deposited 2010-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 45 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, EVAPORATION
Resolution 2.75 Å R-free 0.259
3LZ0 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 1) Deposited 2010-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K cacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.318
3LZ1 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 2) Deposited 2010-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；Kcacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.319
3MGP Binding of Cobalt ions to the Nucleosome Core Particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded CL CHLORIDE ION × 4 CO COBALT (II) ION × 43 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 2.44 Å R-free 0.282
3MGQ Binding of Nickel ions to the Nucleosome Core Particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded NI NICKEL (II) ION × 47 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 2.65 Å R-free 0.276
3MGR Binding of Rubidium ions to the Nucleosome Core Particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded CL CHLORIDE ION × 4 RB RUBIDIUM ION × 5 MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 2.30 Å R-free 0.267
3MGS Binding of Cesium ions to the Nucleosome Core particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded CL CHLORIDE ION × 4 CS CESIUM ION × 12 MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 3.15 Å R-free 0.238
3MNN A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core Deposited 2010-04-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RU RUTHENIUM ION × 3 MML 1-methyl-4-(1-methylethyl)benzene × 3 PTW 1,3,5-triaza-7-phosphatricyclo[3.3.1.1~3,7~]decane × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；55mM KCl, 85mM MnCl2, 20mM K-Cacodylate, pH 6, VAPOR DIFFUSION, temperature 291K
Resolution 2.50 Å R-free 0.277
3MVD Crystal structure of the chromatin factor RCC1 in complex with the nucleosome core particle Deposited 2010-05-04 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；294 K；25 mM sodium acetate buffer, 25 mM sodium citrate, 1 mM DTT, 6 % PEG2000-MME, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 2.90 Å R-free 0.215
3O62 Nucleosome core particle modified with a cisplatin 1,3-cis-{Pt(NH3)2}2+-d(GpTpG) intrastrand cross-link Deposited 2010-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded CPT Cisplatin × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；40-46 mM MnCl2, 30-45 mM KCl, and 20 mM potassium cacodylate pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.22 Å R-free 0.306
3REH 2.5 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Deposited 2011-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；KCl, MnCl2, K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.50 Å R-free 0.270
3REI 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride Deposited 2011-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded PT PLATINUM (II) ION × 49 SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.65 Å R-free 0.276
3REJ 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Deposited 2011-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 13 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.55 Å R-free 0.262
3REK 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Oxaliplatin Deposited 2011-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 2 PT PLATINUM (II) ION × 40 SO4 SULFATE ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å R-free 0.281
3REL 2.7 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Triamminechloroplatinum(II) Chloride Deposited 2011-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 2 PT PLATINUM (II) ION × 48 SO4 SULFATE ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.302
3TU4 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Deposited 2011-09-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.241
3TU4 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Deposited 2011-09-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.241
3UT9 Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601' Derivative (NCP-601L) Deposited 2011-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 29 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.20 Å R-free 0.289
3UTA Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence Containing Two TTAAA elements (NCP-TA2) Deposited 2011-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.07 Å R-free 0.266
3UTB Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite Sequence (NCP146b) Deposited 2011-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 21 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.20 Å R-free 0.275
4EO5 Yeast Asf1 bound to H3/H4G94P mutant Deposited 2012-04-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 21–103（83 aa） Fragment：residues 20-102
Mutation：G94P ACT ACETATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；298 K；7.14% PEG 3350, 0.2 M Magnesium Acetate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.35 Å R-free 0.240
4J8U X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)osmium(II) Deposited 2013-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SO4 SULFATE ION × 3 ELJ chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)osmium(II) × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.38 Å R-free 0.280
4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain B 2–103（102 aa）
Not recorded SO4 SULFATE ION × 1 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.58 Å R-free 0.273
4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain F 2–103（102 aa）
Not recorded SO4 SULFATE ION × 2 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.58 Å R-free 0.273
4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SO4 SULFATE ION × 3 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.58 Å R-free 0.273
4J8W X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) Deposited 2013-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SO4 SULFATE ION × 3 1MK chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.41 Å R-free 0.275
4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain B 2–103（102 aa）
Not recorded SO4 SULFATE ION × 1 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.87 Å R-free 0.280
4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain F 2–103（102 aa）
Not recorded SO4 SULFATE ION × 2 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.87 Å R-free 0.280
4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SO4 SULFATE ION × 3 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.87 Å R-free 0.280
4KGC Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM Deposited 2013-04-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded HRU (ethane-1,2-diamine-kappa~2~N,N')[(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)cyclohexane-1,2,3,4,5,6-hexayl]ruthenium × 4 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.69 Å R-free 0.282
4LD9 Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle Deposited 2013-06-24 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293.15 K；50 mM MES pH 6.5, 12% PEG 400, 12 mM MnCl2, 100 mM NaCl, 10 mM EDTA, VAPOR DIFFUSION, temperature 293.15K
Resolution 3.31 Å R-free 0.295
4R8P Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle Deposited 2014-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions Modified micro batch under oil；pH 7.5；294 K；25 mM HEPES pH 7.5, 80 mM NH4NO3, 3 % PEG2000-MME, Modified micro batch under oil, temperature 294K
Resolution 3.28 Å R-free 0.245
4WU8 Structure of trPtNAP-NCP145 Deposited 2014-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded CX3 [2-(3-{bis[2-(amino-kappaN)ethyl]amino-kappaN}propyl)-1H-benzo[de]isoquinoline-1,3(2H)-dionato(2-)]platinum(1+) × 2 SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.45 Å R-free 0.263
4WU9 Structure of cisPtNAP-NCP145 Deposited 2014-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 CX8 [2-{3-[(2-{[2-(amino-kappaN)ethyl]amino-kappaN}ethyl)amino-kappaN]propyl}-1H-benzo[de]isoquinoline-1,3(2H)-dionato(3-)]platinum × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.60 Å R-free 0.273
4XUJ Nucleosome core particle containing adducts from treatment with a thiomorpholine-substituted [(eta-6-p-cymene)Ru(3-hydroxy-2-pyridone)Cl] compound Deposited 2015-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa） Fragment：UNP residues 2-103
Chain F 2–103（102 aa） Fragment：UNP residues 2-103
Not recorded SO4 SULFATE ION × 3 4A6 [(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)benzene]ruthenium × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40mM MnCl2, 30mM KCl, 20mM K-Cacodylate
Resolution 3.18 Å R-free 0.299
4XZQ Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-02-04 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 25–103（79 aa） Fragment：residues 25-103
Chain F 25–103（79 aa） Fragment：residues 25-103
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292.15 K；potassium chloride, potassium cacodylate, manganese chloride
Resolution 2.40 Å R-free 0.299
4YS3 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-03-16 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 25–103（79 aa） Fragment：residues 25-103
Chain F 25–103（79 aa） Fragment：residues 25-103
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；292.15 K；postassium chloride, manganese chloride, cacodylate
Resolution 3.00 Å R-free 0.279
4Z66 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-04-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 22–103（82 aa）
Chain F 22–103（82 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292.15 K；potassium chloride, potassium cacodylate, manganese chloride
Resolution 2.50 Å R-free 0.296
4ZBJ UBN1 peptide bound to H3.3/H4/Asf1 Deposited 2015-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 21–103（83 aa） Fragment：UNP residues 21-103
Not recorded CL CHLORIDE ION × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.1 M Sodium Cacodylate pH 6.0, 8% PEG 8K, 0.2 M NaCl
Resolution 2.25 Å R-free 0.235
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
Resolution 3.82 Å R-free 0.256
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
Resolution 3.82 Å R-free 0.256
5BS7 Structure of histone H3/H4 in complex with Spt2 Deposited 2015-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 2–103（102 aa）
Chain D 2–103（102 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；0.02 M NaCl, 0.2 M HEPES 7.5, 1.5 M ammonium sulfate
Resolution 3.30 Å R-free 0.290
5BSA Structure of histone H3/H4 in complex with Spt2 Deposited 2015-06-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 2–103（102 aa）
Chain D 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；0.02 M NaCl, 0.2 M HEPES 7.5, 1.6 M ammonium sulfate
Resolution 4.61 Å R-free 0.329
5CP6 Nucleosome Core Particle with Adducts from the Anticancer Compound, [(eta6-5,8,9,10-tetrahydroanthracene)Ru(ethylenediamine)Cl][PF6] Deposited 2015-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded RUH (ethane6-5,8,9,10-tetrahydroanthracene)Ru(II)(ethylene-diamine)Cl × 3 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.251
5DNM Nucleosome core particle containing adducts of ruthenium(II)-toluene PTA complex Deposited 2015-09-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RAX dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate
Resolution 2.81 Å R-free 0.241
5DNN Nucleosome core particle containing adducts of gold(I)-triethylphosphane and ruthenium(II)-toluene PTA complexes Deposited 2015-09-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded AUF triethylphosphanuidylgold(1+) × 2 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RAX dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate
Resolution 2.80 Å R-free 0.236
5E5A Crystal structure of the chromatin-tethering domain of Human cytomegalovirus IE1 protein bound to the nucleosome core particle Deposited 2015-10-08 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；289 K；sodium cacodylate, magnesium acetate, 2-methyl-2,4-pentanediol
Resolution 2.81 Å R-free 0.242
5F99 X-ray Structure of the MMTV-A Nucleosome Core Particle Deposited 2015-12-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：H18R Mutation：H18R CL CHLORIDE ION × 4 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；sample was mixed 1:1 with 10 mM K-cacodylate, pH 6.0, 180 mM MgCl2, 50 mM KCl and equilibrated against a 1:4 dilution of the same solution
Resolution 2.63 Å R-free 0.252
5HQ2 Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle Deposited 2016-01-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: hexadecameric
Chain B 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 5.5；277 K；25 mM sodium acetate pH 5.5, 40 mM sodium citrate,1 mM DTT, 6% PEG2000-MME
Resolution 4.50 Å R-free 0.397
5KGF Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution Deposited 2016-06-13 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Mutation：K20C Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K20C Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；High concentration NCP-ubme/GST-53BP1 complex at 200 mM salt was diluted just prior to grid freezing.
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；Plunged into liquid ethane-propane (FEI VITROBOT MARK III)
Resolution 4.54 Å
5MLU Crystal structure of the PFV GAG CBS bound to a mononucleosome Deposited 2016-12-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 20–103（84 aa）
Chain F 20–103（84 aa）
Not recorded MN MANGANESE (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.05M MnCl2, 0.04M KCl, 0.1M potassium cacodylate pH 6.0, 5% trehalose, 24% MPD
Resolution 2.80 Å R-free 0.252
5NL0 Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1 Deposited 2017-04-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293.15 K；Mix of equal volumes of the nucleosome/H1 complex (25-30 microM) and a crystallization solution composed of MPD (6% v/v), 50 mM NaCl, and 50 mM sodium potassium phosphate pH 6.4.
Resolution 5.40 Å R-free 0.265
5NL0 Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1 Deposited 2017-04-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain L 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293.15 K；Mix of equal volumes of the nucleosome/H1 complex (25-30 microM) and a crystallization solution composed of MPD (6% v/v), 50 mM NaCl, and 50 mM sodium potassium phosphate pH 6.4.
Resolution 5.40 Å R-free 0.265
5O9G Structure of nucleosome-Chd1 complex Deposited 2017-06-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
5OMX X-ray Structure of the H2A-N38C Nucleosome Core Particle Deposited 2017-08-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 33 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；8 mg/ml sample was mixed 1:1 with 10 mM K-Cacodylate (pH 6.0), 140-150 mM MnCl2, 100 KCl. and equilibrated against a 1:4 dilution of the same solution
Resolution 2.32 Å R-free 0.259
5ONG X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer Deposited 2017-08-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 20 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；Sample was mixed in a 1:1 ratio with 10 mM Na-cacodylate, pH 6.0, 130-180 mM MnCl2, 100-160 mM KCl and equilibrated against a 1:4 dilution of the same solution
Resolution 2.80 Å R-free 0.247
5ONW X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two H2A/H2B dimers crosslinked via H2A N38C Deposited 2017-08-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MN MANGANESE (II) ION × 20 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；Sample was mixed in a 1:1 ratio with 10 mM Na-cacodylate, pH 6.0, 160-210 mM MnCl2, 140-200 mM KCl and equilibrated against a 1:4 dilution of the same solution
Resolution 2.80 Å R-free 0.254
5OXV Structure of the 4_601_157 tetranucleosome (C2 form) Deposited 2017-09-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Chain L 2–103（102 aa）
Chain P 2–103（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；30-60 mM KCl, 90-110 mM MgCl2 and 5 mM Na-cacodylate, pH 6
Resolution 6.72 Å R-free 0.352
5OY7 Structure of the 4_601_157 tetranucleosome (P1 form) Deposited 2017-09-07 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 × 32 PDB declaration: 34-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Chain J 2–103（102 aa）
Chain N 2–103（102 aa）
Chain R 2–103（102 aa）
Chain V 2–103（102 aa）
Chain Z 2–103（102 aa）
Chain d 2–103（102 aa）
Not recorded CL CHLORIDE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；30-60 mM KCl, 90-110 mM MgCl2 and 5 mM Na-cacodyalte, pH 6.0
Resolution 5.77 Å R-free 0.238
5X0X Complex of Snf2-Nucleosome complex with Snf2 bound to position +6 of the nucleosome Deposited 2017-01-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
5X0Y Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome Deposited 2017-01-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.69 Å
5XF6 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 EDN ETHANE-1,2-DIAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0
Resolution 2.63 Å R-free 0.254
5Z3L Structure of Snf2-nucleosome complex in apo state Deposited 2018-01-08 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.31 Å
5Z3O Structure of Snf2-nucleosome complex in ADP state Deposited 2018-01-08 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
5Z3U Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state Deposited 2018-01-08 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.31 Å
5Z3V Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state Deposited 2018-01-08 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.22 Å
6ESF Nucleosome : Class 1 Deposited 2017-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ESG Nucleosome breathing : Class 2 Deposited 2017-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.40 Å
6ESH Nucleosome breathing : Class 3 Deposited 2017-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
6ESI Nucleosome breathing : Class 4 Deposited 2017-10-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
6FQ5 Class 1 : canonical nucleosome Deposited 2018-02-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 19–102（84 aa）
Chain F 19–103（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6FQ6 Class 2 : distorted nucleosome Deposited 2018-02-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 19–103（85 aa）
Chain F 19–103（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6FQ8 Class 3 : translocated nucleosome Deposited 2018-02-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 18–103（86 aa）
Chain F 18–103（86 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6FTX Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome Deposited 2018-02-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6G0L Structure of two molecules of the chromatin remodelling enzyme Chd1 bound to a nucleosome Deposited 2018-03-19 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 10.00 Å
6I84 Structure of transcribing RNA polymerase II-nucleosome complex Deposited 2018-11-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain O 1–103（103 aa）
Chain U 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6IRO the crosslinked complex of ISWI-nucleosome in the ADP-bound state Deposited 2018-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6IY2 Structure of Snf2-MMTV-A nucleosome complex at shl2 in ADP state Deposited 2018-12-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 16–103（88 aa）
Chain F 16–103（88 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
6IY3 Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state Deposited 2018-12-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 16–103（88 aa）
Chain F 16–103（88 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.67 Å
6J99 Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome Deposited 2019-01-22 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6JM9 cryo-EM structure of DOT1L bound to unmodified nucleosome Deposited 2019-03-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.30 Å
6JMA cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome Deposited 2019-03-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6JYL The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state Deposited 2019-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE；blot 1.5s
Resolution 3.37 Å
6K1P The complex of ISWI-nucleosome in the ADP.BeF-bound state Deposited 2019-05-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5；10 mM Tris, 50 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1.5s
Resolution 3.87 Å
6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIW Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIX Cryo-EM structure of human MLL1-NCP complex, binding mode1 Deposited 2019-07-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6KIZ Cryo-EM structure of human MLL1-NCP complex, binding mode2 Deposited 2019-07-20 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6KW3 The ClassA RSC-Nucleosome Complex Deposited 2019-09-05 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain B 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.13 Å
6KW4 The ClassB RSC-Nucleosome Complex Deposited 2019-09-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain B 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.55 Å
6KW5 The ClassC RSC-Nucleosome Complex Deposited 2019-09-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain S 1–103（103 aa）
Chain W 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 10.13 Å
6LTJ Structure of nucleosome-bound human BAF complex Deposited 2020-01-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6NE3 Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at SHL-2 Deposited 2018-12-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；2.5 ul of nucleosome-443 SNF2h complexes were applied to a glow discharged Quantifoil holey carbon grid (1.2 um hole size, 400 mesh), blotted in a Vitrobot Mark I (FEI Company) using 6 seconds blotting at 100% humidity, and then plunge-frozen in liquid ethane cooled by liquid nitrogen.
Resolution 3.90 Å
6NJ9 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex Deposited 2019-01-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing.
Resolution 2.96 Å
6NN6 Structure of Dot1L-H2BK120ub nucleosome complex Deposited 2019-01-14 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6NOG Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome Deposited 2019-01-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing
Resolution 3.90 Å
6NQA Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex Deposited 2019-01-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing.
Resolution 3.54 Å
6NZO Set2 bound to nucleosome Deposited 2019-02-14 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6O22 Structure of Asf1-H3:H4-Rtt109-Vps75 histone chaperone-lysine acetyltransferase complex with the histone substrate. Deposited 2019-02-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule Experimental method not declared
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition 70 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 70 uM Rtt109, 70 uM Asf1, 70 uM H3, 70 uM H4, 100% D2O | 100% D2O
NMR sample composition 70 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 70 uM Rtt109, 70 uM Asf1, 70 uM H3(110A,63C) mutant with a cysteine coupled to a paramagnetic tag, 70 uM H4, 100% D2O | 100% D2O
NMR sample composition 90 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 90 uM Rtt109, 90 uM Asf1, 90 uM H3(110A,76C) mutant with a cysteine coupled to a paramagnetic tag, 90 uM H4, 100% D2O | 100% D2O
NMR sample composition 30 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 30 uM Rtt109, 30 uM Asf1, 30 uM H3, 30 uM H4(30C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2O | 100% D2O
NMR sample composition 70 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 70 uM Rtt109, 70 uM Asf1, 70 uM H3, 70 uM H4(82C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2O | 100% D2O
NMR sample composition 80 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 80 uM Rtt109, 80 uM Asf1, 80 uM H3, 80 uM H4(45C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2O | 100% D2O
NMR sample composition 30 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 30 uM Rtt109, 30 uM Asf1, 30 uM H3, 30 uM H4(93C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2O | 100% D2O
Resolution not provided
6O96 Dot1L bound to the H2BK120 Ubiquitinated nucleosome Deposited 2019-03-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen PROPANE；blotted for 3s before plunging
Resolution 3.50 Å
6OM3 Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle Deposited 2019-04-18 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277.15 K；6 mM Na-Cacodylate pH 6.0, 0.4 mM Spermine-HCl, 2 mM MgCl2 and 1.75% v/v PEG 400
Resolution 3.30 Å R-free 0.250
6OM3 Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle Deposited 2019-04-18 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain N 1–103（103 aa）
Chain R 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277.15 K；6 mM Na-Cacodylate pH 6.0, 0.4 mM Spermine-HCl, 2 mM MgCl2 and 1.75% v/v PEG 400
Resolution 3.30 Å R-free 0.250
6PA7 The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. Deposited 2019-06-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded CL CHLORIDE ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain H 1–103（103 aa）
Chain L 1–103（103 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
6PWW Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain H 1–103（103 aa）
Chain L 1–103（103 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6PWX Cryo-EM structure of RbBP5 bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain H 1–103（103 aa）
Chain L 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6PX1 Set2 bound to nucleosome Deposited 2019-07-24 Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6PX3 Set2 bound to nucleosome Deposited 2019-07-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6R1U Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2 Deposited 2019-03-15 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.36 Å
6RYR Nucleosome-CHD4 complex structure (single CHD4 copy) Deposited 2019-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6RYU Nucleosome-CHD4 complex structure (two CHD4 copies) Deposited 2019-06-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6S01 Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome Deposited 2019-06-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.20 Å
6T9L SAGA DUB module bound to a ubiqitinated nucleosome Deposited 2019-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.60 Å
6TDA Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome Deposited 2019-11-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.00 Å
6TEM CENP-A nucleosome core particle with 145 base pairs of the Widom 601 sequence by cryo-EM Deposited 2019-11-12 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6UGM Structural basis of COMPASS eCM recognition of an unmodified nucleosome Deposited 2019-09-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6UH5 Structural basis of COMPASS eCM recognition of the H2Bub nucleosome Deposited 2019-09-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6UXW SWI/SNF nucleosome complex with ADP-BeFx Deposited 2019-11-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain S 2–103（102 aa）
Chain W 2–103（102 aa）
Not recorded PO4 PHOSPHATE ION × 12 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM HEPES, pH 7.9, 10 mM MgCl2, 50 mM KCl, 1 mM DTT, 5% glycerol, 0.05% NP-40
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.96 Å
6VEN Yeast COMPASS in complex with a ubiquitinated nucleosome Deposited 2020-01-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 5 3.5 sec blot time
Resolution 3.37 Å
6VYP Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate Deposited 2020-02-27 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 7.5；277 K；25 mM HEPES pH7.5, 75 mM triammonium citrate, 10% PEG2000-MME, Modified Microbatch under oil
Resolution 4.99 Å R-free 0.277
6VYP Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate Deposited 2020-02-27 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 7.5；277 K；25 mM HEPES pH7.5, 75 mM triammonium citrate, 10% PEG2000-MME, Modified Microbatch under oil
Resolution 4.99 Å R-free 0.277
6VZ4 Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state Deposited 2020-02-27 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；4 second blot time, blot force 20
Resolution 3.90 Å
6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain H 1–103（103 aa）
Chain L 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6W5N Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Deposited 2020-03-13 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain H 1–103（103 aa）
Chain L 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
6WKR PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome Deposited 2020-04-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: octadecameric
Chain J 1–103（103 aa）
Chain Q 1–103（103 aa）
Not recorded MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6WZ5 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-13 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
6WZ9 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-13 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6X0N Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-16 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 23-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 10.00 Å
6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain D 21–103（83 aa）
Chain I 21–103（83 aa）
Not recorded GOL GLYCEROL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
Resolution 2.35 Å R-free 0.233
6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain N 21–103（83 aa）
Chain S 21–103（83 aa）
Not recorded GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
Resolution 2.35 Å R-free 0.233
6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain X 21–103（83 aa）
Chain c 21–103（83 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
Resolution 2.35 Å R-free 0.233
6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain h 21–103（83 aa）
Chain m 21–103（83 aa）
Not recorded GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
Resolution 2.35 Å R-free 0.233
6Z6P HDAC-PC-Nuc Deposited 2020-05-28 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 21–103（83 aa）
Chain F 26–103（78 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.43 Å
6ZHX Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: nucleosome class. Deposited 2020-06-24 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot time 2.5 s, blot force 0. Two sample applications and blots were performed before vitrification.
Resolution 2.50 Å
6ZHY Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: hexasome class. Deposited 2020-06-24 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot time 2.5 s, blot force 0. Two sample applications and blots were performed before vitrification.
Resolution 3.00 Å
7AT8 Histone H3 recognition by nucleosome-bound PRC2 subunit EZH2. Deposited 2020-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain E 2–103（102 aa）
Chain I 2–103（102 aa）
Not recorded ZN ZINC ION × 7 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.40 Å
7CRO NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP Deposited 2020-08-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.75 Å
7CRP NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode) Deposited 2020-08-14 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7CRQ NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode) Deposited 2020-08-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 2 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.15 Å
7CRR Native NSD3 bound to 187-bp nucleosome Deposited 2020-08-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.48 Å
7E8I Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin Deposited 2021-03-01 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7EG6 Snf5 Finger Helix bound to the nucleosome Deposited 2021-03-24 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7EGP The structure of SWI/SNF-nucleosome complex Deposited 2021-03-24 Different construct Different oligomeric state Different ligand/ion Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain P 2–103（102 aa）
Chain T 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
7ENN The structure of ALC1 bound to the nucleosome Deposited 2021-04-18 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain F 2–103（102 aa）
Chain L 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7K6P Active state Dot1 bound to the unacetylated H4 nucleosome Deposited 2020-09-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 14–103（90 aa）
Chain F 14–103（90 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7K6Q Active state Dot1 bound to the H4K16ac nucleosome Deposited 2020-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 12–103（92 aa）
Chain F 12–103（92 aa）
Mutation：K17X Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K17X Non-standard monomer：Yes (specific site not provided by mmCIF) SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7KBD Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction) Deposited 2020-10-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
7KBE Nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction) Deposited 2020-10-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7KBF H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction) Deposited 2020-10-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.42 Å
7KTQ Nucleosome from a dimeric PRC2 bound to a nucleosome Deposited 2020-11-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 25–103（79 aa）
Chain F 25–103（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7M1X Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z Deposited 2021-03-15 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4.5 seconds before plunging
Resolution 3.70 Å
7MBM Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Deposited 2021-04-01 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain H 1–103（103 aa）
Chain L 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.76 Å
7MBN Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Deposited 2021-04-01 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain H 1–103（103 aa）
Chain L 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
7NKX RNA polymerase II-Spt4/5-nucleosome-Chd1 structure Deposited 2021-02-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7NKY RNA Polymerase II-Spt4/5-nucleosome-FACT structure Deposited 2021-02-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 27-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7OH9 Nucleosome with TBP and TFIIA bound at SHL -6 Deposited 2021-05-09 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7OHA nucleosome with TBP and TFIIA bound at SHL +2 Deposited 2021-05-09 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7OHB TBP-nucleosome complex Deposited 2021-05-10 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHC Cryo-EM structure of nucleosome core particle composed of the Widom 601 DNA sequence Deposited 2021-05-10 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7OTQ Cryo-EM structure of ALC1/CHD1L bound to a PARylated nucleosome Deposited 2021-06-10 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 uL were applied on grid and immediately blotted for 2.5 s at blot force 0.
Resolution 4.80 Å
7SSA Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome Deposited 2021-11-10 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7SWY 2.6 A structure of a 40-601[TA-rich+1]-40 nucleosome Deposited 2021-11-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM HEPES, pH 7.0, 60 mM KCl, 1.5 mM DTT, 1 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
7TN2 Composite model of a Chd1-nucleosome complex in the nucleotide-free state derived from 2.3A and 2.7A Cryo-EM maps Deposited 2022-01-20 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM HEPES, pH 7.0, 60 mM KCl, 1.5 mM DTT, 1 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
7UNC Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 29 PDB declaration: 32-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7UND Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) Deposited 2022-04-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7UNK Structure of Importin-4 bound to the H3-H4-ASF1 histone-histone chaperone complex Deposited 2022-04-11 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
7UX9 Arabidopsis DDM1 bound to nucleosome (H2A.W, H2B, H3.3, H4, with 147 bp DNA) Deposited 2022-05-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain G 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Blotted for 2.5 seconds before plunging.
Resolution 3.20 Å
7VDT The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex Deposited 2021-09-07 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7VDV The overall structure of human chromatin remodeling PBAF-nucleosome complex Deposited 2021-09-07 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7X3T Cryo-EM structure of ISW1a-dinucleosome Deposited 2022-03-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.40 Å
7X3V Cryo-EM structure of IOC3-N2 nucleosome Deposited 2022-03-01 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
7X3W Cryo-EM structure of ISW1-N1 nucleosome Deposited 2022-03-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7X3X Cryo-EM structure of N1 nucleosome-RA Deposited 2022-03-01 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7XFC Structure of nucleosome-DI complex (-30I, Apo state) Deposited 2022-04-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.90 Å
7XFH Structure of nucleosome-AAG complex (A-30I, post-catalytic state) Deposited 2022-04-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.90 Å
7XFI Structure of nucleosome-DI complex (-50I, Apo state) Deposited 2022-04-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.90 Å
7XFJ Structure of nucleosome-AAG complex (T-50I, post-catalytic state) Deposited 2022-04-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.00 Å
7XFL Structure of nucleosome-AAG complex (A-53I, free state) Deposited 2022-04-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.80 Å
7XFM Structure of nucleosome-AAG complex (A-53I, post-catalytic state) Deposited 2022-04-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.10 Å
7XFN Structure of nucleosome-DI complex (-55I, Apo state) Deposited 2022-04-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.80 Å
7XNP Structure of nucleosome-AAG complex (A-55I, post-catalytic state) Deposited 2022-04-29 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.90 Å
7YI1 Cryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome Deposited 2022-07-14 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7YI4 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in close state Deposited 2022-07-14 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain H 2–103（102 aa）
Chain L 2–103（102 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
7YI5 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in loose state Deposited 2022-07-14 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain H 2–103（102 aa）
Chain L 2–103（102 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
7YRD histone methyltransferase Deposited 2022-08-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7YRG histone methyltransferase Deposited 2022-08-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 SAM S-ADENOSYLMETHIONINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain b 2–103（102 aa）
Chain f 2–103（102 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
8A3Y Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex Deposited 2022-06-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 27 PDB declaration: 30-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8B0A Cryo-EM structure of ALC1 bound to an asymmetric, site-specifically PARylated nucleosome Deposited 2022-09-07 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Mutation：0 Mutation：0 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8BZ1 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Deposited 2022-12-14 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
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 3.80 Å
8CBN structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Deposited 2023-01-25 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
8CBQ structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Deposited 2023-01-25 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8CEO Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Deposited 2023-02-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain s 2–103（102 aa）
Chain w 2–103（102 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8DU4 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Deposited 2022-07-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
8ETT Class1 of the INO80-Hexasome complex Deposited 2022-10-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 6.68 Å
8ETV Class2 of the INO80-Hexasome complex Deposited 2022-10-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.16 Å
8EU2 Class3 of the INO80-Hexasome complex Deposited 2022-10-18 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 2.93 Å
8F86 SIRT6 bound to an H3K9Ac nucleosome Deposited 2022-11-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZSL [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3aR,5R,6R,6aR)-6-hydroxytetrahydro-2H-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8G57 Structure of nucleosome-bound Sirtuin 6 deacetylase Deposited 2023-02-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 19–103（85 aa）
Chain F 19–103（85 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；12.5 mM HEPES pH 7.5, 60 mM KCl, 1.5% glycerol, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8G6G H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 5 Deposited 2023-02-15 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
8G6H H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 6 Deposited 2023-02-15 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
8G6Q H2AK119ub-modified nucleosome ubiquitin position 1 Deposited 2023-02-15 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.41 Å
8G6S H2AK119ub-modified nucleosome ubiquitin position 2 Deposited 2023-02-15 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
8G86 Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of nucleosome) Deposited 2023-02-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
8G88 Human Oct4 bound to nucleosome with human nMatn1 sequence Deposited 2023-02-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
8G8B Nucleosome with human nMatn1 sequence in complex with Human Oct4 Deposited 2023-02-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
8G8G Interaction of H3 tail in LIN28B nucleosome with Oct4 Deposited 2023-02-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8GPN Human menin in complex with H3K79Me2 nucleosome Deposited 2022-08-26 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain NB 1–103（103 aa）
Chain NF 1–103（103 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain NB 1–103（103 aa）
Chain NF 1–103（103 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å
8KD2 Rpd3S in complex with 187bp nucleosome Deposited 2023-08-09 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain P 2–103（102 aa）
Chain T 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8KD3 Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA Deposited 2023-08-09 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain P 2–103（102 aa）
Chain T 2–103（102 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8KD4 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1 Deposited 2023-08-09 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain P 2–103（102 aa）
Chain T 2–103（102 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
8KD5 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2 Deposited 2023-08-09 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain P 2–103（102 aa）
Chain T 2–103（102 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8KD6 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3 Deposited 2023-08-09 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain P 2–103（102 aa）
Chain T 2–103（102 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8KD7 Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA Deposited 2023-08-09 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain P 2–103（102 aa）
Chain T 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8OF4 Nucleosome Bound human SIRT6 (Composite) Deposited 2023-03-13 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
8PC5 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex Deposited 2023-06-09 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8PC6 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Deposited 2023-06-09 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8PEO H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex Deposited 2023-06-14 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
8PEP H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Deposited 2023-06-14 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
8RUP Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome Deposited 2024-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；3 s blotting time, -10 force, no wait time.
Resolution 2.42 Å
8RUQ Borealin N-terminus in complex with H3.T3p-nucleosome Deposited 2024-01-31 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；3 s blotting time, -10 force, no wait time.
Resolution 2.29 Å
8SVF BAP1/ASXL1 bound to the H2AK119Ub Nucleosome Deposited 2023-05-16 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8T3T Structure of Bre1-nucleosome complex - state3 Deposited 2023-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.21 Å
8T3W Structure of Bre1-nucleosome complex - state2 Deposited 2023-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
8T3Y Structure of Bre1-nucleosome complex - state1 Deposited 2023-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES, pH 7.5, 50 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
8T9G Automethylated PRC2 dimer bound to nucleosome Deposited 2023-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain J 1–103（103 aa）
Chain X 1–103（103 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
8TAS PRC2 monomer bound to nucleosome Deposited 2023-06-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain J 1–103（103 aa）
Chain X 1–103（103 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8TB9 PRC2-J119-450 monomer bound to H1-nucleosome Deposited 2023-06-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain J 1–103（103 aa）
Chain X 1–103（103 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8UXQ Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome Deposited 2023-11-09 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain F 2–103（102 aa）
Chain L 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
8V4Y Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 1) Deposited 2023-11-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8V6V Cryo-EM structure of doubly-bound SNF2h-nucleosome complex Deposited 2023-12-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8V7L Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 2) Deposited 2023-12-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8VX5 Nucleosome core particle containing an 8-oxoG damage site Deposited 2024-02-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8VX6 Human OGG1 bound at the nucleosomal DNA entry site Deposited 2024-02-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8XJV Structural basis for the linker histone H5-nucleosome binding and chromatin compaction Deposited 2023-12-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 108 PDB declaration: 110-meric
Chain 0 1–103（103 aa）
Chain 1 1–103（103 aa）
Chain 2 1–103（103 aa）
Chain 3 1–103（103 aa）
Chain 4 1–103（103 aa）
Chain 5 1–103（103 aa）
Chain 6 1–103（103 aa）
Chain 7 1–103（103 aa）
Chain 8 1–103（103 aa）
Chain 9 1–103（103 aa）
Chain CD 1–103（103 aa）
Chain a2 1–103（103 aa）
Chain a3 1–103（103 aa）
Chain a4 1–103（103 aa）
Chain a5 1–103（103 aa）
Chain a6 1–103（103 aa）
Chain a7 1–103（103 aa）
Chain a8 1–103（103 aa）
Chain a9 1–103（103 aa）
Chain v 1–103（103 aa）
Chain w 1–103（103 aa）
Chain x 1–103（103 aa）
Chain y 1–103（103 aa）
Chain z 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.60 Å
9B2S Haspin bound to nucleosome in position 1 Deposited 2024-03-16 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
9B2T Haspin bound to nucleosome in position 2 Deposited 2024-03-16 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å
9B3P The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome Deposited 2024-03-19 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；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
9C9G S.c INO80 in complex with S.c 0/80 nucleosome Deposited 2024-06-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 2.91 Å
9C9S S.c INO80 in complex with S.c 0/40 nucleosome, Class 1 Deposited 2024-06-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.09 Å
9C9T S.c INO80 in complex with S.c 0/40 nucleosome, Class 2 Deposited 2024-06-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.16 Å
9C9X S.c INO80 in complex with Xenopus 0/80 nucleosome, Nucleosome Deposited 2024-06-16 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 2.83 Å
9CA7 Cryo-EM structure of human SRCAP-nucleosome complex in the fully-engaged state (composite structure) Deposited 2024-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain V 2–103（102 aa）
Chain X 2–103（102 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 5 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
9CA8 Cryo-EM structure of human SRCAP-nucleosome complex in the partially-engaged state (composite structure) Deposited 2024-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain V 2–103（102 aa）
Chain X 2–103（102 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 5 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
9CAA Cryo-EM structure of human SRCAP-nucleosome complex in the pre-engaged state (composite structure) Deposited 2024-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain V 2–103（102 aa）
Chain X 2–103（102 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.04 Å
9CAB Cryo-EM structure of human SRCAP-nucleosome complex in the encounter state (composite structure) Deposited 2024-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain V 2–103（102 aa）
Chain X 2–103（102 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 5 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.94 Å
9CAU DeltaArp8 INO80 bound to S.c 0/40 nucleosome, Nucleosome Deposited 2024-06-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 4.18 Å
9CB7 DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, Ino80-Nucleosome Deposited 2024-06-18 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 4.04 Å
9CG9 Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2 Deposited 2024-06-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 uL of sample was applied to grid.
Resolution 2.94 Å
9DBY ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome Deposited 2024-08-24 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9DDE ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome Deposited 2024-08-28 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9DG3 ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome Deposited 2024-09-01 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9DGG ncPRC1RYBP bound to unmodified nucleosome Deposited 2024-09-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9E1L Snf2h bound nucleosome complex - ClassA1 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
9E1M Snf2h bound nucleosome complex - ClassA2 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
9E1N Snf2h bound nucleosome complex-ClassA3 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9E1O Snf2h bound nucleosome complex - ClassB1 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E1P Snf2h bound nucleosome complex - ClassB2 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
9E1Q Snf2h bound nucleosome complex - ClassB3 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9E1R Snf2h bound nucleosome complex - ClassB4 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9E1U Snf2h bound nucleosome complex - ClassC1 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9E1V Snf2h bound nucleosome complex - ClassC2 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9E1W Snf2h bound nucleosome complex - ClassC3 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9E1X Snf2h bound nucleosome complex - ClassD1 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9E1Y Empty Nucleosome with 601 widom sequence Deposited 2024-10-21 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EAR CHD1-nucleosome complex (closed state) Deposited 2024-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 18–103（86 aa）
Chain F 18–103（86 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9EGX RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 29 PDB declaration: 32-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9EGY RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9EGZ RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 12 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9EH0 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9EH1 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream Deposited 2024-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain b 25–102（78 aa）
Chain f 25–102（78 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9EH2 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9EIL SIRT6 bound to an H3K27Ac nucleosome Deposited 2024-11-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded ZSL [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3aR,5R,6R,6aR)-6-hydroxytetrahydro-2H-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9F0O The molecular basis and modulation of lamin-specific chromatin interaction Deposited 2024-04-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 21–103（83 aa）
Chain F 21–103（83 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9GD0 Structure of a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9GD1 Structure of Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9GD2 Structure of Chd1 bound to a dinucleosome with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9GD3 Structure of a mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA. Deposited 2024-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9GEN Recombinant Myeloperoxidase bound to nucleosome core particle Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.76 Å
9GEO Nucleosome core particle Deposited 2024-08-07 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.79 Å
9GEP Native monomeric Myeloperoxidase bound to nucleosome core particle Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
9GEQ Native dimeric Myeloperoxidase bound to nucleosome core particle; composite map Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded CL CHLORIDE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9GER Native dimeric Myeloperoxidase bound to nucleosome core particle, intermediate state; composite map Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded CL CHLORIDE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.58 Å
9IGJ structure of two human ELF2 transcription factors in complex with a nucleosome Deposited 2025-02-19 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；1 mM EDTA, 30 mM NaCl, 2 mM DTT in 20 mM HEPES, pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9IHD Nucleosome core particle bound by one molecule of DTT-reduced native monomeric myeloperoxidase Deposited 2025-02-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
9IHE Nucleosome core particle bound by two molecules of DTT-reduced native monomeric myeloperoxidase Deposited 2025-02-21 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9IHF Nucleosome core particle bound by one monomer and one dimer of of DTT-reduced native myeloperoxidase Deposited 2025-02-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain B 17–103（87 aa）
Chain F 17–103（87 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9JAO The structure of SMARCAD1 bound to the hexasome in the presence of ADP-BeFx Deposited 2024-08-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9LJ2 Structure of isw1-nucleosome double-bound complex in ADP-ADP+ state Deposited 2025-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 16–103（88 aa）
Chain F 16–103（88 aa）
Not recorded MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9M76 UHRF1 bound to a mononucleosome in its pre-active state, with the RING domain bound to the SRA domain. Deposited 2025-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
9M77 The activated state of human UHRF1 bound to a mononucleosome, with the finger loop ordered and linker 4 disordered. Deposited 2025-03-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9MPP The cryo-EM structure of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L Deposited 2024-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 6 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9N6H 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex Deposited 2025-02-05 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 16–103（88 aa）
Chain F 16–103（88 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.54 Å
9N6I 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex Deposited 2025-02-05 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 16–103（88 aa）
Chain F 16–103（88 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.61 Å
9N6K 2.88 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex with DNA-binding domain Deposited 2025-02-05 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 16–103（88 aa）
Chain F 16–103（88 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9NH8 CHD1-nucleosome complex (anchored state) Deposited 2025-02-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ARG ARGININE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9NY4 USP21 bound to H2AK119ub nucleosome Deposited 2025-03-26 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9Q7U Composite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer bound to 167H3K36me2-nucleosome Deposited 2025-08-25 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded ZN ZINC ION × 9 SAO 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9QAJ Structure of the nucleosome-bound human BCL7A Deposited 2025-02-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9R5K Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-09 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Hepes, 120mM Nacl
cryo-EM vitrification conditions Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity
Resolution 4.20 Å
9R5S Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-09 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Hepes, 120mM Nacl
cryo-EM vitrification conditions Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity
Resolution 3.80 Å
9R5W Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-10 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Hepes, 120mM Nacl
cryo-EM vitrification conditions Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity
Resolution 3.80 Å
9SI3 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome Deposited 2025-08-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
9SI9 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class0) Deposited 2025-08-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
9SJ5 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class1) Deposited 2025-08-29 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
9SLJ Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Double Occupancy) Deposited 2025-09-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9T4V ALC1/CHD1L in an intermediate conformation, bound to a PARylated nucleosome Deposited 2025-11-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 uL were applied on grid and immediately blotted for 2.5 s at blot force 0.
Resolution 6.60 Å
9UX9 local ATPase-NCP structure of the ncBAF-nucleosome complex in the ADP-BeFx-bound state Deposited 2025-05-13 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9UXA local ARP-NCP structure of the ncBAF-nucleosome complex in the apo state Deposited 2025-05-13 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
9V2V Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome Deposited 2025-05-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain R 23–101（79 aa）
Chain V 23–101（79 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9V2W Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome Deposited 2025-05-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain L 23–101（79 aa）
Chain R 23–101（79 aa）
Chain V 23–101（79 aa）
Chain Z 23–101（79 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9V33 Calypso/Asx/NCP-ub complex Deposited 2025-05-21 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 5.90 Å
9V9Q Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.80 Å
9V9R Cryo-EM structure of the ncPRC1.1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å
9V9S Cryo-EM structure of the ncPRC1.1 complex bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.80 Å
9V9T Cryo-EM structure of the ncPRC1.6 complex bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.90 Å
9V9U Cryo-EM structure of the ncPRC1.4 complex containing two RNF2-BMI1 bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.70 Å
9V9V Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.80 Å
9V9W Cryo-EM structure of the ncPRC1.4 complex containing two RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
9V9X Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.30 Å
9V9Y Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å
9V9Z Cryo-EM structure of the ncPRC1.4 complex containing one RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
9W74 Cryo-EM structure of the close-packed di-hexasome (CPDH) Deposited 2025-08-05 Different construct Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain L 1–103（103 aa）
Chain P 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.94 Å
9WBZ The structure of NCP-motor-ARP module of ncBAF-nucleosome complex Deposited 2025-08-15 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9WC0 The structure of NCP-RA module of ncBAF-nucleosome complex Deposited 2025-08-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
9XYC Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome LEDGF+nucleosome map Q Deposited 2025-08-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain b 1–103（103 aa）
Chain f 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9Y4P Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker Deposited 2025-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Chain R 1–103（103 aa）
Chain X 1–103（103 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.84 Å

354 other PDB entries and 370 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H4_XENLA
Isoform —
PDB entities 6
Chains and sequence ranges Author chain H； PDBConstruct 1–103； UniProt 1–103 Author chain L； PDBConstruct 1–103； UniProt 1–103

Histone H2A

Xenopus laevis

UniProt Q6AZJ8

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–DNA Heteromer Protein × 12 DNA 2 PDB declaration: tetradecameric（14） Consistent with all polymer counts Chain I； UniProt 2–130 Chain M； UniProt 2–130 Not recorded Retinoblastoma-binding protein 5 × 1 （Q15291） WD repeat-containing protein 5 × 1 （P61964） Histone-lysine N-methyltransferase 2A × 1 （Q03164） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2B 1.1 × 2 （P02281） DNA (147-MER) × 1 DNA (147-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.90 Å

Other States of the Same Protein in the Database

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

Other PDB Difference from Current Entry 6W5I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1S32 Molecular Recognition of the Nucleosomal 'Supergroove' Deposited 2004-01-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–120（119 aa）
Chain G 2–120（119 aa）
Not recorded MN MANGANESE (II) ION × 14 IMT 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID × 4 PYB 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID × 12 ABU GAMMA-AMINO-BUTANOIC ACID × 2 BAL BETA-ALANINE × 2 DIB 3-AMINO-(DIMETHYLPROPYLAMINE) × 2 OGG 2-(2-CARBAMOYLMETHOXY-ETHOXY)-ACETAMIDE × 1 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；Manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.05 Å R-free 0.243
21VV Cryo-EM structure of ncBAF bound to the nucleosome Deposited 2025-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 100 mM KCl, 2 mM MgCl2, 2 mM DTT, 0.5 mM ADP, 8 mM NaF, 1 mM BeSO4.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
21WA Cryo-EM structure of the ATPase domain of SMARCA4 bound to a nucleosome Deposited 2025-12-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 100 mM KCl, 2 mM MgCl2, 2 mM DTT, 0.5 mM ADP, 8 mM NaF, 1 mM BeSO4.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
21WC Cryo-EM structure of the ATPase domain of SMARCA4 and the finger helix of BCL7A bound to a nucleosome Deposited 2025-12-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM HEPES pH 8.0, 100 mM KCl, 2 mM MgCl2, 2 mM DTT, 0.5 mM ADP, 8 mM NaF, 1 mM BeSO4.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
2NZD Nucleosome core particle containing 145 bp of DNA Deposited 2006-11-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–120（119 aa）
Chain G 2–120（119 aa）
Not recorded MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.65 Å R-free 0.283
3B6F Nucleosome core particle treated with cisplatin Deposited 2007-10-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K
Resolution 3.45 Å R-free 0.402
3B6G Nucleosome core particle treated with oxaliplatin Deposited 2007-10-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K
Resolution 3.45 Å R-free 0.435
3KUY DNA Stretching in the Nucleosome Facilitates Alkylation by an Intercalating Antitumor Agent Deposited 2009-11-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–120（119 aa）
Chain G 2–120（119 aa）
Not recorded MN MANGANESE (II) ION × 1 ATV 2-[(2R)-oxiran-2-ylmethyl]-1H-benzo[de]isoquinoline-1,3(2H)-dione × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6；291 K；85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, EVAPORATION
Resolution 2.90 Å R-free 0.286
3KWQ Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Deposited 2009-12-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–121（107 aa） Fragment：UNP residues 15-121
Chain G 15–121（107 aa） Fragment：UNP residues 15-121
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.50 Å R-free 0.315
3KXB Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Deposited 2009-12-02 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；Crystals were grown by vapor diffusion in 8 20 days at 20 C using a droplet containing 4.0 mg ml−1 core particle 50 mM KCl, 70 75 mM MnCl , and 20 mM potassium cacodylate, pH 6.0, surrounded by silicon oil DC200 (110mPa s; Fluka) and equilibrated against 40 46 mM MnCl2, 35 40 mM KCl and 20 mM potassium cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 293K
Resolution 3.20 Å R-free 0.292
3LEL Structural Insight into the Sequence-Dependence of Nucleosome Positioning Deposited 2010-01-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85mM MnCl2, 60mM KCl, 20mM K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.300
3LEL Structural Insight into the Sequence-Dependence of Nucleosome Positioning Deposited 2010-01-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 2–130（129 aa）
Chain Q 2–130（129 aa）
Not recorded MN MANGANESE (II) ION × 19 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85mM MnCl2, 60mM KCl, 20mM K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.300
3LJA Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome Deposited 2010-01-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 45 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, EVAPORATION
Resolution 2.75 Å R-free 0.259
3LZ0 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 1) Deposited 2010-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–120（119 aa） Fragment：residues 2-120
Chain G 2–120（119 aa） Fragment：residues 2-120
Not recorded MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K cacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.318
3LZ1 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 2) Deposited 2010-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–120（119 aa） Fragment：residues 2-120
Chain G 2–120（119 aa） Fragment：residues 2-120
Not recorded MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；Kcacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.319
3MGP Binding of Cobalt ions to the Nucleosome Core Particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–120（119 aa） Fragment：UNP RESIDUES 2-120
Chain G 2–120（119 aa） Fragment：UNP RESIDUES 2-120
Not recorded CL CHLORIDE ION × 4 CO COBALT (II) ION × 43 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 2.44 Å R-free 0.282
3MGQ Binding of Nickel ions to the Nucleosome Core Particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–120（119 aa） Fragment：UNP RESIDUES 2-120
Chain G 2–120（119 aa） Fragment：UNP RESIDUES 2-120
Not recorded NI NICKEL (II) ION × 47 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 2.65 Å R-free 0.276
3MGR Binding of Rubidium ions to the Nucleosome Core Particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–120（119 aa） Fragment：UNP RESIDUES 2-120
Chain G 2–120（119 aa） Fragment：UNP RESIDUES 2-120
Not recorded CL CHLORIDE ION × 4 RB RUBIDIUM ION × 5 MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 2.30 Å R-free 0.267
3MGS Binding of Cesium ions to the Nucleosome Core particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–120（119 aa） Fragment：UNP RESIDUES 2-120
Chain G 2–120（119 aa） Fragment：UNP RESIDUES 2-120
Not recorded CL CHLORIDE ION × 4 CS CESIUM ION × 12 MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 3.15 Å R-free 0.238
3MNN A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core Deposited 2010-04-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–120（119 aa）
Chain G 2–120（119 aa）
Not recorded SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RU RUTHENIUM ION × 3 MML 1-methyl-4-(1-methylethyl)benzene × 3 PTW 1,3,5-triaza-7-phosphatricyclo[3.3.1.1~3,7~]decane × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；55mM KCl, 85mM MnCl2, 20mM K-Cacodylate, pH 6, VAPOR DIFFUSION, temperature 291K
Resolution 2.50 Å R-free 0.277
3MVD Crystal structure of the chromatin factor RCC1 in complex with the nucleosome core particle Deposited 2010-05-04 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；294 K；25 mM sodium acetate buffer, 25 mM sodium citrate, 1 mM DTT, 6 % PEG2000-MME, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 2.90 Å R-free 0.215
3TU4 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Deposited 2011-09-15 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.241
3TU4 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Deposited 2011-09-15 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.241
3UT9 Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601' Derivative (NCP-601L) Deposited 2011-11-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 29 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.20 Å R-free 0.289
3UTA Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence Containing Two TTAAA elements (NCP-TA2) Deposited 2011-11-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.07 Å R-free 0.266
3UTB Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite Sequence (NCP146b) Deposited 2011-11-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MN MANGANESE (II) ION × 21 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.20 Å R-free 0.275
4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain C 2–130（129 aa）
Not recorded SO4 SULFATE ION × 1 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.58 Å R-free 0.273
4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain G 2–130（129 aa）
Not recorded SO4 SULFATE ION × 2 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.58 Å R-free 0.273
4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SO4 SULFATE ION × 3 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.58 Å R-free 0.273
4J8W X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) Deposited 2013-02-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SO4 SULFATE ION × 3 1MK chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.41 Å R-free 0.275
4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain C 2–130（129 aa）
Not recorded SO4 SULFATE ION × 1 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.87 Å R-free 0.280
4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain G 2–130（129 aa）
Not recorded SO4 SULFATE ION × 2 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.87 Å R-free 0.280
4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SO4 SULFATE ION × 3 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.87 Å R-free 0.280
4KGC Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM Deposited 2013-04-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded HRU (ethane-1,2-diamine-kappa~2~N,N')[(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)cyclohexane-1,2,3,4,5,6-hexayl]ruthenium × 4 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.69 Å R-free 0.282
4KHA Structural basis of histone H2A-H2B recognition by the essential chaperone FACT Deposited 2013-04-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 15–103（89 aa） Fragment：UNP residues 15-103
Not recorded CL CHLORIDE ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；manual setup 1ul protein (15 mg / ml) plus 1 ul crystallization buffer (7.25% [vol/vol] PEG8000, 0.2 M MgCl2, 0.1 M Tris pH 7.8), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.35 Å R-free 0.229
4LD9 Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle Deposited 2013-06-24 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293.15 K；50 mM MES pH 6.5, 12% PEG 400, 12 mM MnCl2, 100 mM NaCl, 10 mM EDTA, VAPOR DIFFUSION, temperature 293.15K
Resolution 3.31 Å R-free 0.295
4R8P Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle Deposited 2014-09-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions Modified micro batch under oil；pH 7.5；294 K；25 mM HEPES pH 7.5, 80 mM NH4NO3, 3 % PEG2000-MME, Modified micro batch under oil, temperature 294K
Resolution 3.28 Å R-free 0.245
4XUJ Nucleosome core particle containing adducts from treatment with a thiomorpholine-substituted [(eta-6-p-cymene)Ru(3-hydroxy-2-pyridone)Cl] compound Deposited 2015-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa） Fragment：UNP residues 2-126
Chain G 2–130（129 aa） Fragment：UNP residues 2-126
Not recorded SO4 SULFATE ION × 3 4A6 [(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)benzene]ruthenium × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40mM MnCl2, 30mM KCl, 20mM K-Cacodylate
Resolution 3.18 Å R-free 0.299
4XZQ Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-02-04 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–121（107 aa） Fragment：residues 15-121
Chain G 15–121（107 aa） Fragment：residues 15-121
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292.15 K；potassium chloride, potassium cacodylate, manganese chloride
Resolution 2.40 Å R-free 0.299
4YS3 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-03-16 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–121（107 aa） Fragment：residues 15-121
Chain G 15–121（107 aa） Fragment：residues 15-121
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；292.15 K；postassium chloride, manganese chloride, cacodylate
Resolution 3.00 Å R-free 0.279
4Z66 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-04-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 15–121（107 aa）
Chain G 15–121（107 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292.15 K；potassium chloride, potassium cacodylate, manganese chloride
Resolution 2.50 Å R-free 0.296
5CP6 Nucleosome Core Particle with Adducts from the Anticancer Compound, [(eta6-5,8,9,10-tetrahydroanthracene)Ru(ethylenediamine)Cl][PF6] Deposited 2015-07-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded RUH (ethane6-5,8,9,10-tetrahydroanthracene)Ru(II)(ethylene-diamine)Cl × 3 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.251
5DNM Nucleosome core particle containing adducts of ruthenium(II)-toluene PTA complex Deposited 2015-09-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RAX dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate
Resolution 2.81 Å R-free 0.241
5DNN Nucleosome core particle containing adducts of gold(I)-triethylphosphane and ruthenium(II)-toluene PTA complexes Deposited 2015-09-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded AUF triethylphosphanuidylgold(1+) × 2 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RAX dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate
Resolution 2.80 Å R-free 0.236
5E5A Crystal structure of the chromatin-tethering domain of Human cytomegalovirus IE1 protein bound to the nucleosome core particle Deposited 2015-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；289 K；sodium cacodylate, magnesium acetate, 2-methyl-2,4-pentanediol
Resolution 2.81 Å R-free 0.242
5HQ2 Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle Deposited 2016-01-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: hexadecameric
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 5.5；277 K；25 mM sodium acetate pH 5.5, 40 mM sodium citrate,1 mM DTT, 6% PEG2000-MME
Resolution 4.50 Å R-free 0.397
5O9G Structure of nucleosome-Chd1 complex Deposited 2017-06-19 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
5OMX X-ray Structure of the H2A-N38C Nucleosome Core Particle Deposited 2017-08-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Mutation：N38C Mutation：N38C MN MANGANESE (II) ION × 33 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；8 mg/ml sample was mixed 1:1 with 10 mM K-Cacodylate (pH 6.0), 140-150 mM MnCl2, 100 KCl. and equilibrated against a 1:4 dilution of the same solution
Resolution 2.32 Å R-free 0.259
5ONG X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer Deposited 2017-08-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MN MANGANESE (II) ION × 20 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；Sample was mixed in a 1:1 ratio with 10 mM Na-cacodylate, pH 6.0, 130-180 mM MnCl2, 100-160 mM KCl and equilibrated against a 1:4 dilution of the same solution
Resolution 2.80 Å R-free 0.247
5ONW X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two H2A/H2B dimers crosslinked via H2A N38C Deposited 2017-08-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Mutation：N38C Mutation：N38C MN MANGANESE (II) ION × 20 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；Sample was mixed in a 1:1 ratio with 10 mM Na-cacodylate, pH 6.0, 160-210 mM MnCl2, 140-200 mM KCl and equilibrated against a 1:4 dilution of the same solution
Resolution 2.80 Å R-free 0.254
5OXV Structure of the 4_601_157 tetranucleosome (C2 form) Deposited 2017-09-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；30-60 mM KCl, 90-110 mM MgCl2 and 5 mM Na-cacodylate, pH 6
Resolution 6.72 Å R-free 0.352
5OY7 Structure of the 4_601_157 tetranucleosome (P1 form) Deposited 2017-09-07 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 × 32 PDB declaration: 34-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain K 1–130（130 aa）
Chain O 1–130（130 aa）
Chain S 1–130（130 aa）
Chain W 1–130（130 aa）
Chain a 1–130（130 aa）
Chain e 1–130（130 aa）
Not recorded CL CHLORIDE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；30-60 mM KCl, 90-110 mM MgCl2 and 5 mM Na-cacodyalte, pH 6.0
Resolution 5.77 Å R-free 0.238
5X0X Complex of Snf2-Nucleosome complex with Snf2 bound to position +6 of the nucleosome Deposited 2017-01-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
5X0Y Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome Deposited 2017-01-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.69 Å
5XF6 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker Deposited 2017-04-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 EDN ETHANE-1,2-DIAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0
Resolution 2.63 Å R-free 0.254
5Z3L Structure of Snf2-nucleosome complex in apo state Deposited 2018-01-08 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.31 Å
5Z3O Structure of Snf2-nucleosome complex in ADP state Deposited 2018-01-08 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
5Z3U Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state Deposited 2018-01-08 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.31 Å
5Z3V Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state Deposited 2018-01-08 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.22 Å
6ESF Nucleosome : Class 1 Deposited 2017-10-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ESG Nucleosome breathing : Class 2 Deposited 2017-10-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.40 Å
6ESH Nucleosome breathing : Class 3 Deposited 2017-10-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
6ESI Nucleosome breathing : Class 4 Deposited 2017-10-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
6FQ5 Class 1 : canonical nucleosome Deposited 2018-02-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 10–119（110 aa）
Chain G 10–119（110 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6FQ6 Class 2 : distorted nucleosome Deposited 2018-02-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 10–119（110 aa）
Chain G 10–119（110 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6FQ8 Class 3 : translocated nucleosome Deposited 2018-02-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 10–119（110 aa）
Chain G 10–119（110 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6IRO the crosslinked complex of ISWI-nucleosome in the ADP-bound state Deposited 2018-11-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6IY2 Structure of Snf2-MMTV-A nucleosome complex at shl2 in ADP state Deposited 2018-12-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 10–122（113 aa）
Chain G 10–122（113 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
6IY3 Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state Deposited 2018-12-12 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 10–122（113 aa）
Chain G 10–122（113 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.67 Å
6J99 Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome Deposited 2019-01-22 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6JM9 cryo-EM structure of DOT1L bound to unmodified nucleosome Deposited 2019-03-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 15–121（107 aa）
Chain G 15–121（107 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.30 Å
6JMA cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome Deposited 2019-03-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 15–130（116 aa）
Chain G 15–130（116 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6JYL The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state Deposited 2019-04-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE；blot 1.5s
Resolution 3.37 Å
6K01 Crystal structure of xH2A-H2B Deposited 2019-05-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 15–106（92 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Ammonium sulfate, 0.1M HEPES pH=7.5, 25% PEG 3350
Resolution 2.84 Å R-free 0.278
6K1P The complex of ISWI-nucleosome in the ADP.BeF-bound state Deposited 2019-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5；10 mM Tris, 50 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1.5s
Resolution 3.87 Å
6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIW Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIX Cryo-EM structure of human MLL1-NCP complex, binding mode1 Deposited 2019-07-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6KIZ Cryo-EM structure of human MLL1-NCP complex, binding mode2 Deposited 2019-07-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6KW3 The ClassA RSC-Nucleosome Complex Deposited 2019-09-05 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain O 1–130（130 aa）
Chain S 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.13 Å
6KW4 The ClassB RSC-Nucleosome Complex Deposited 2019-09-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain O 1–130（130 aa）
Chain S 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.55 Å
6KW5 The ClassC RSC-Nucleosome Complex Deposited 2019-09-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain O 1–130（130 aa）
Chain T 1–130（130 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 10.13 Å
6N1Z Importin-9 bound to H2A-H2B Deposited 2018-11-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–130（130 aa） Fragment：HISTONE H2A
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.04 M MES, 0.11 M potassium acetate, 2 mM magnesium acetate, 2 mM DTT, 3.0 M potassium formate, 25% glycerol
Resolution 2.70 Å R-free 0.238
6N1Z Importin-9 bound to H2A-H2B Deposited 2018-11-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–130（130 aa） Fragment：HISTONE H2A
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.04 M MES, 0.11 M potassium acetate, 2 mM magnesium acetate, 2 mM DTT, 3.0 M potassium formate, 25% glycerol
Resolution 2.70 Å R-free 0.238
6NZO Set2 bound to nucleosome Deposited 2019-02-14 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 18–130（113 aa）
Chain G 18–130（113 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6O96 Dot1L bound to the H2BK120 Ubiquitinated nucleosome Deposited 2019-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：G99R, A123S Mutation：G99R, A123S SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen PROPANE；blotted for 3s before plunging
Resolution 3.50 Å
6OM3 Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle Deposited 2019-04-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：G99R, S123A Mutation：G99R, S123A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277.15 K；6 mM Na-Cacodylate pH 6.0, 0.4 mM Spermine-HCl, 2 mM MgCl2 and 1.75% v/v PEG 400
Resolution 3.30 Å R-free 0.250
6OM3 Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle Deposited 2019-04-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain O 1–130（130 aa）
Chain S 1–130（130 aa）
Mutation：G99R, S123A Mutation：G99R, S123A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277.15 K；6 mM Na-Cacodylate pH 6.0, 0.4 mM Spermine-HCl, 2 mM MgCl2 and 1.75% v/v PEG 400
Resolution 3.30 Å R-free 0.250
6PX1 Set2 bound to nucleosome Deposited 2019-07-24 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain C 18–130（113 aa）
Chain G 18–130（113 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6PX3 Set2 bound to nucleosome Deposited 2019-07-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 18–130（113 aa）
Chain G 18–130（113 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6R1T Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 1, free nuclesome Deposited 2019-03-15 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 11–121（111 aa）
Chain G 11–121（111 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
6R1U Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2 Deposited 2019-03-15 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.36 Å
6R25 Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3 Deposited 2019-03-15 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.61 Å
6S01 Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome Deposited 2019-06-13 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.20 Å
6T9L SAGA DUB module bound to a ubiqitinated nucleosome Deposited 2019-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.60 Å
6TDA Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome Deposited 2019-11-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.00 Å
6TEM CENP-A nucleosome core particle with 145 base pairs of the Widom 601 sequence by cryo-EM Deposited 2019-11-12 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6UGM Structural basis of COMPASS eCM recognition of an unmodified nucleosome Deposited 2019-09-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain C 13–119（107 aa）
Chain G 13–119（107 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6UH5 Structural basis of COMPASS eCM recognition of the H2Bub nucleosome Deposited 2019-09-26 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain C 13–119（107 aa）
Chain G 13–119（107 aa）
Not recorded ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6VZ4 Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state Deposited 2020-02-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；4 second blot time, blot force 20
Resolution 3.90 Å
6WZ5 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-13 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
6WZ9 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-13 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6X0N Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-16 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 23-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 10.00 Å
6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 14–119（106 aa）
Chain F 14–119（106 aa）
Not recorded GOL GLYCEROL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
Resolution 2.35 Å R-free 0.233
6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain K 14–119（106 aa）
Chain P 14–119（106 aa）
Not recorded GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
Resolution 2.35 Å R-free 0.233
6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain U 14–119（106 aa）
Chain Z 14–119（106 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
Resolution 2.35 Å R-free 0.233
6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain e 14–119（106 aa）
Chain j 14–119（106 aa）
Not recorded GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
Resolution 2.35 Å R-free 0.233
6Z6P HDAC-PC-Nuc Deposited 2020-05-28 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 17–119（103 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.43 Å
7AT8 Histone H3 recognition by nucleosome-bound PRC2 subunit EZH2. Deposited 2020-10-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 2–130（129 aa）
Chain J 2–130（129 aa）
Not recorded ZN ZINC ION × 7 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.40 Å
7CRO NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP Deposited 2020-08-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.75 Å
7CRP NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode) Deposited 2020-08-14 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7CRQ NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode) Deposited 2020-08-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 2 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.15 Å
7CRR Native NSD3 bound to 187-bp nucleosome Deposited 2020-08-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
Resolution 3.48 Å
7E8I Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin Deposited 2021-03-01 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Mutation：K16C Mutation：K16C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7EA5 Yeast Set2 bound to a nucleosome containing oncohistone mutations Deposited 2021-03-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 14–118（105 aa）
Chain G 14–118（105 aa）
Not recorded ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7EGP The structure of SWI/SNF-nucleosome complex Deposited 2021-03-24 Different oligomeric state Different ligand/ion Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain Q 2–130（129 aa）
Chain U 2–130（129 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
7KTQ Nucleosome from a dimeric PRC2 bound to a nucleosome Deposited 2020-11-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 14–118（105 aa）
Chain G 14–118（105 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7MBM Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Deposited 2021-04-01 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain I 2–130（129 aa）
Chain M 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.76 Å
7MBN Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Deposited 2021-04-01 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain I 2–130（129 aa）
Chain M 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
7OH9 Nucleosome with TBP and TFIIA bound at SHL -6 Deposited 2021-05-09 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7OHA nucleosome with TBP and TFIIA bound at SHL +2 Deposited 2021-05-09 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7OHB TBP-nucleosome complex Deposited 2021-05-10 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHC Cryo-EM structure of nucleosome core particle composed of the Widom 601 DNA sequence Deposited 2021-05-10 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
7UNC Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome Deposited 2022-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 29 PDB declaration: 32-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7UND Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) Deposited 2022-04-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7VDT The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7VDV The overall structure of human chromatin remodeling PBAF-nucleosome complex Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7VVU NuA4 HAT module bound to the nucleosome Deposited 2021-11-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain N 1–130（130 aa）
Chain S 1–130（130 aa）
Not recorded CMC CARBOXYMETHYL COENZYME *A × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.40 Å
7VVZ NuA4 bound to the nucleosome Deposited 2021-11-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain N 1–130（130 aa）
Chain S 1–130（130 aa）
Not recorded CMC CARBOXYMETHYL COENZYME *A × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.80 Å
7X3T Cryo-EM structure of ISW1a-dinucleosome Deposited 2022-03-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Chain M 1–130（130 aa）
Chain Q 1–130（130 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.40 Å
7X3V Cryo-EM structure of IOC3-N2 nucleosome Deposited 2022-03-01 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
7X3W Cryo-EM structure of ISW1-N1 nucleosome Deposited 2022-03-01 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7X3X Cryo-EM structure of N1 nucleosome-RA Deposited 2022-03-01 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7XPX Cryo-EM structure of the histone methyltransferase SET8 bound to H4K20Ecx-nucleosome Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7YI1 Cryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome Deposited 2022-07-14 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7YI4 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in close state Deposited 2022-07-14 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain I 2–130（129 aa）
Chain M 2–130（129 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
7YI5 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in loose state Deposited 2022-07-14 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain I 2–130（129 aa）
Chain M 2–130（129 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
8A3Y Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex Deposited 2022-06-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 27 PDB declaration: 30-meric
Chain c 17–119（103 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8CBN structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Deposited 2023-01-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
8CBQ structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Deposited 2023-01-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8CEO Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain t 2–130（129 aa）
Chain x 2–130（129 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8DU4 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Deposited 2022-07-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
8ETT Class1 of the INO80-Hexasome complex Deposited 2022-10-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain C 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 6.68 Å
8ETV Class2 of the INO80-Hexasome complex Deposited 2022-10-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain C 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.16 Å
8EU2 Class3 of the INO80-Hexasome complex Deposited 2022-10-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain C 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 2.93 Å
8EUE Class1 of the INO80-Nucleosome complex Deposited 2022-10-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.48 Å
8EUJ Class2 of the INO80-Nucleosome complex Deposited 2022-10-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.36 Å
8G6G H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 5 Deposited 2023-02-15 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
8G6H H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 6 Deposited 2023-02-15 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
8G6Q H2AK119ub-modified nucleosome ubiquitin position 1 Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：K119C Mutation：K119C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.41 Å
8G6S H2AK119ub-modified nucleosome ubiquitin position 2 Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：K119C Mutation：K119C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
8G86 Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of nucleosome) Deposited 2023-02-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
8G88 Human Oct4 bound to nucleosome with human nMatn1 sequence Deposited 2023-02-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
8G8B Nucleosome with human nMatn1 sequence in complex with Human Oct4 Deposited 2023-02-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
8G8G Interaction of H3 tail in LIN28B nucleosome with Oct4 Deposited 2023-02-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8HXY Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Deposited 2023-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8HXZ Cryo-EM structure of Eaf3 CHD in complex with nucleosome Deposited 2023-01-05 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8HY0 Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Deposited 2023-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8IHM Eaf3 CHD domain bound to the nucleosome Deposited 2023-02-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.58 Å
8IHT Rpd3S bound to the nucleosome Deposited 2023-02-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 1 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.72 Å
8JHO Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome Deposited 2023-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Chain c 2–130（129 aa）
Chain g 2–130（129 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
8KD2 Rpd3S in complex with 187bp nucleosome Deposited 2023-08-09 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain Q 2–130（129 aa）
Chain U 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8KD3 Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA Deposited 2023-08-09 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain Q 2–130（129 aa）
Chain U 2–130（129 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8KD4 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1 Deposited 2023-08-09 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain Q 2–130（129 aa）
Chain U 2–130（129 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
8KD5 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2 Deposited 2023-08-09 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain Q 2–130（129 aa）
Chain U 2–130（129 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8KD6 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3 Deposited 2023-08-09 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain Q 2–130（129 aa）
Chain U 2–130（129 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8KD7 Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA Deposited 2023-08-09 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain Q 2–130（129 aa）
Chain U 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8PC5 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex Deposited 2023-06-09 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8PC6 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Deposited 2023-06-09 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8PEO H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex Deposited 2023-06-14 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
8PEP H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Deposited 2023-06-14 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
8RUQ Borealin N-terminus in complex with H3.T3p-nucleosome Deposited 2024-01-31 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；3 s blotting time, -10 force, no wait time.
Resolution 2.29 Å
8SKZ Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome Deposited 2023-04-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8T9H Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Deposited 2023-06-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
8TAS PRC2 monomer bound to nucleosome Deposited 2023-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain R 1–130（130 aa）
Chain U 1–130（130 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8TOF Rpd3S bound to an H3K36Cme3 modified nucleosome Deposited 2023-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain c 1–130（130 aa）
Chain g 1–130（130 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8U5H Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome Deposited 2023-09-12 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain K 1–130（130 aa）
Chain R 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
8UW1 Cryo-EM structure of DNMT3A1 UDR in complex with H2AK119Ub-nucleosome Deposited 2023-11-05 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8V25 H2BK120ub-modified nucleosome ubiquitin position 1 Deposited 2023-11-21 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
8V26 H2BK120ub-modified nucleosome ubiquitin position 2 Deposited 2023-11-21 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
8V27 H2BK120ub-modified nucleosome ubiquitin position 3 Deposited 2023-11-21 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
8V28 H2BK120ub-modified nucleosome ubiquitin position 4 Deposited 2023-11-22 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
8VMJ H3K4me3 nucleosome bound to PRC2_AJ119-450 Deposited 2024-01-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain K 13–119（107 aa）
Chain R 13–119（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VMN H3K4me3 nucleosome bound to PRC2_AJ1-450 Deposited 2024-01-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain K 13–119（107 aa）
Chain R 13–119（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8VO0 H3K36me3-modified nucleosome bound to PRC2_AJ1-450 with histone H3 tail disengaged Deposited 2024-01-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain K 13–119（107 aa）
Chain R 13–119（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8VX5 Nucleosome core particle containing an 8-oxoG damage site Deposited 2024-02-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8VX6 Human OGG1 bound at the nucleosomal DNA entry site Deposited 2024-02-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8XAA Structure of NAP1 in complex with H2A-H2B Deposited 2023-12-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain I 15–106（92 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris, pH 8.0, 25 % v/v PEG 400
Resolution 3.35 Å R-free 0.261
8XAA Structure of NAP1 in complex with H2A-H2B Deposited 2023-12-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain K 15–106（92 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris, pH 8.0, 25 % v/v PEG 400
Resolution 3.35 Å R-free 0.261
8XJV Structural basis for the linker histone H5-nucleosome binding and chromatin compaction Deposited 2023-12-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 108 PDB declaration: 110-meric
Chain A 1–130（130 aa）
Chain Ae 1–130（130 aa）
Chain B 1–130（130 aa）
Chain C 1–130（130 aa）
Chain D 1–130（130 aa）
Chain E 1–130（130 aa）
Chain F 1–130（130 aa）
Chain G 1–130（130 aa）
Chain H 1–130（130 aa）
Chain I 1–130（130 aa）
Chain K 1–130（130 aa）
Chain L 1–130（130 aa）
Chain aj 1–130（130 aa）
Chain ak 1–130（130 aa）
Chain al 1–130（130 aa）
Chain am 1–130（130 aa）
Chain an 1–130（130 aa）
Chain ao 1–130（130 aa）
Chain ap 1–130（130 aa）
Chain aq 1–130（130 aa）
Chain ar 1–130（130 aa）
Chain as 1–130（130 aa）
Chain at 1–130（130 aa）
Chain au 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.60 Å
9B2S Haspin bound to nucleosome in position 1 Deposited 2024-03-16 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
9B2T Haspin bound to nucleosome in position 2 Deposited 2024-03-16 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å
9C9X S.c INO80 in complex with Xenopus 0/80 nucleosome, Nucleosome Deposited 2024-06-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 2.83 Å
9CAN S.c INO80 in complex with Xenopus 0/40 nucleosome Deposited 2024-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.30 Å
9E1X Snf2h bound nucleosome complex - ClassD1 Deposited 2024-10-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9EAR CHD1-nucleosome complex (closed state) Deposited 2024-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 15–119（105 aa）
Chain G 15–119（105 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9JAO The structure of SMARCAD1 bound to the hexasome in the presence of ADP-BeFx Deposited 2024-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain G 1–130（130 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9JNP Structure of isw1-nucleosome complex in ATP state Deposited 2024-09-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9JNT Structure of isw1-nucleosome complex in ADP* state Deposited 2024-09-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9JNU Structure of isw1-nucleosome complex in ADP state Deposited 2024-09-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9JNV Structure of isw1-nucleosome complex in ADP(S) state Deposited 2024-09-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9JNW Structure of isw1-nucleosome complex in ADP+ state Deposited 2024-09-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9JNX Structure of isw1-nucleosome complex in ADP*+ state Deposited 2024-09-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9JNZ Structure of isw1-nucleosome complex in Apo state Deposited 2024-09-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded CL CHLORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9JO2 Structure of isw1-nucleosome complex in Apo* state Deposited 2024-09-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded CL CHLORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9JO5 Structure of isw1-nucleosome complex in ADP-B state Deposited 2024-09-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9KQ2 Cryo-EM structure of RNF168'-RNF168-UbcH5c complex bound to nucleosome Deposited 2024-11-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9LIU Structure of isw1-nucleosome double-bound complex in ATP-ATP state Deposited 2025-01-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9LJ2 Structure of isw1-nucleosome double-bound complex in ADP-ADP+ state Deposited 2025-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 13–119（107 aa）
Chain G 13–119（107 aa）
Not recorded MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9M76 UHRF1 bound to a mononucleosome in its pre-active state, with the RING domain bound to the SRA domain. Deposited 2025-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
9M77 The activated state of human UHRF1 bound to a mononucleosome, with the finger loop ordered and linker 4 disordered. Deposited 2025-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9N6H 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex Deposited 2025-02-05 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 11–120（110 aa）
Chain G 11–120（110 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.54 Å
9N6I 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex Deposited 2025-02-05 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 11–120（110 aa）
Chain G 11–120（110 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.61 Å
9N6K 2.88 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex with DNA-binding domain Deposited 2025-02-05 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 11–120（110 aa）
Chain G 11–120（110 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9NH8 CHD1-nucleosome complex (anchored state) Deposited 2025-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded ARG ARGININE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9QAJ Structure of the nucleosome-bound human BCL7A Deposited 2025-02-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 2–120（119 aa）
Chain G 2–120（119 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9UX9 local ATPase-NCP structure of the ncBAF-nucleosome complex in the ADP-BeFx-bound state Deposited 2025-05-13 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9UXA local ARP-NCP structure of the ncBAF-nucleosome complex in the apo state Deposited 2025-05-13 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
9V2V Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome Deposited 2025-05-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain O 12–118（107 aa）
Chain S 12–118（107 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9V2W Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome Deposited 2025-05-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain B 12–118（107 aa）
Chain M 12–118（107 aa）
Chain O 12–118（107 aa）
Chain S 12–118（107 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9V33 Calypso/Asx/NCP-ub complex Deposited 2025-05-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 5.90 Å
9V9Q Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.80 Å
9V9R Cryo-EM structure of the ncPRC1.1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å
9V9S Cryo-EM structure of the ncPRC1.1 complex bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：K119C Mutation：K119C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.80 Å
9V9T Cryo-EM structure of the ncPRC1.6 complex bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：K119C Mutation：K119C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.90 Å
9V9U Cryo-EM structure of the ncPRC1.4 complex containing two RNF2-BMI1 bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：K119C Mutation：K119C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.70 Å
9V9V Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：K119C Mutation：K119C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.80 Å
9V9W Cryo-EM structure of the ncPRC1.4 complex containing two RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：K119C Mutation：K119C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
9V9X Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：K119C Mutation：K119C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.30 Å
9V9Y Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：K119C Mutation：K119C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å
9V9Z Cryo-EM structure of the ncPRC1.4 complex containing one RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：K119C Mutation：K119C No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
9WBZ The structure of NCP-motor-ARP module of ncBAF-nucleosome complex Deposited 2025-08-15 Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9WC0 The structure of NCP-RA module of ncBAF-nucleosome complex Deposited 2025-08-15 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å

226 other PDB entries and 238 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q6AZJ8_XENLA
Isoform —
PDB entities 7
Chains and sequence ranges Author chain I； PDBConstruct 4–132； UniProt 2–130 Author chain M； PDBConstruct 4–132； UniProt 2–130

Histone H2B 1.1

Xenopus laevis

UniProt P02281

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–DNA Heteromer Protein × 12 DNA 2 PDB declaration: tetradecameric（14） Consistent with all polymer counts Chain J； UniProt 5–126 Chain N； UniProt 5–126 Not recorded Retinoblastoma-binding protein 5 × 1 （Q15291） WD repeat-containing protein 5 × 1 （P61964） Histone-lysine N-methyltransferase 2A × 1 （Q03164） Set1/Ash2 histone methyltransferase complex subunit ASH2 × 1 （Q9UBL3） Histone H3.2 × 2 （P84233） Histone H4 × 2 （P62799） Histone H2A × 2 （Q6AZJ8） DNA (147-MER) × 1 DNA (147-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 6.90 Å

Other States of the Same Protein in the Database

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

Other PDB Difference from Current Entry 6W5I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AOI COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) AND 146 BP LONG DNA FRAGMENT Deposited 1997-07-03 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 D 27–125（99 aa） Fragment：HISTONE H2B
Chain H 27–125（99 aa） Fragment：HISTONE H2B
Mutation：A7P Mutation：A7P MN MANGANESE (II) ION × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å R-free 0.302
1F66 2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z Deposited 2000-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.60 Å R-free 0.249
1KX3 X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution Deposited 2002-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded MN MANGANESE (II) ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.275
1KX4 X-Ray Structure of the Nucleosome Core Particle, NCP146b, at 2.6 A Resolution Deposited 2002-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.60 Å R-free 0.300
1KX5 X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution Deposited 2002-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded MN MANGANESE (II) ION × 14 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.94 Å R-free 0.275
1M18 LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA Deposited 2002-06-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded MN MANGANESE (II) ION × 11 1SZ N-[5-[[4-[[5-[[5-[[5-[[5-[[3-[3-(dimethylamino)propylamino]-3-oxidanylidene-propyl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]amino]-4-oxidanylidene-butyl]carbamoyl]-1-methyl-pyrrol-3-yl]-1-methyl-4-[[1-methyl-4-[(1-methylimidazol-2-yl)carbonylamino]pyrrol-2-yl]carbonylamino]imidazole-2-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；Manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.45 Å R-free 0.257
1P34 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.70 Å R-free 0.270
1P3A Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.00 Å R-free 0.260
1P3B Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.00 Å R-free 0.286
1P3F Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.90 Å R-free 0.272
1P3G Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.70 Å R-free 0.265
1P3I Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.30 Å R-free 0.275
1P3K Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.90 Å R-free 0.291
1P3L Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.40 Å R-free 0.265
1P3M Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.90 Å R-free 0.270
1P3O Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.75 Å R-free 0.276
1P3P Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.70 Å R-free 0.268
1ZBB Structure of the 4_601_167 Tetranucleosome Deposited 2005-04-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 36-meric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Chain d 1–125（125 aa）
Chain h 1–125（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.75；294 K；magnesium chloride, potassium chloride, potassium cacodylate, trisCl, pH 6.75, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 9.00 Å
2F8N 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes Deposited 2005-12-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain H 4–125（122 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；34 to 37.5mM KCl and 40-45mM MnCl2, 5mM Potassium Cacodylate, Sample concentration: 8-12 mg/ml, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.90 Å R-free 0.269
2FJ7 Crystal structure of Nucleosome Core Particle Containing a Poly (dA.dT) Sequence Element Deposited 2005-12-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；20 to 35 mM KCl, 34 to 48 mM MnCl2, and 5mM K-cacodylate pH 6.0 , VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.20 Å R-free 0.350
2NZD Nucleosome core particle containing 145 bp of DNA Deposited 2006-11-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–125（125 aa）
Chain H 1–125（125 aa）
Not recorded MN MANGANESE (II) ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.65 Å R-free 0.283
3B6F Nucleosome core particle treated with cisplatin Deposited 2007-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K
Resolution 3.45 Å R-free 0.402
3B6G Nucleosome core particle treated with oxaliplatin Deposited 2007-10-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K
Resolution 3.45 Å R-free 0.435
3KWQ Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Deposited 2009-12-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 34–126（93 aa） Fragment：UNP residues 34-126
Chain H 34–126（93 aa） Fragment：UNP residues 34-126
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.50 Å R-free 0.315
3KXB Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Deposited 2009-12-02 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S33T Mutation：S33T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；Crystals were grown by vapor diffusion in 8 20 days at 20 C using a droplet containing 4.0 mg ml−1 core particle 50 mM KCl, 70 75 mM MnCl , and 20 mM potassium cacodylate, pH 6.0, surrounded by silicon oil DC200 (110mPa s; Fluka) and equilibrated against 40 46 mM MnCl2, 35 40 mM KCl and 20 mM potassium cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 293K
Resolution 3.20 Å R-free 0.292
3LEL Structural Insight into the Sequence-Dependence of Nucleosome Positioning Deposited 2010-01-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85mM MnCl2, 60mM KCl, 20mM K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.300
3LEL Structural Insight into the Sequence-Dependence of Nucleosome Positioning Deposited 2010-01-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain N 2–126（125 aa）
Chain R 2–126（125 aa）
Not recorded MN MANGANESE (II) ION × 19 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85mM MnCl2, 60mM KCl, 20mM K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.95 Å R-free 0.300
3LJA Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome Deposited 2010-01-26 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 D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 45 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, EVAPORATION
Resolution 2.75 Å R-free 0.259
3LZ0 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 1) Deposited 2010-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K cacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.318
3LZ1 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 2) Deposited 2010-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；Kcacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.319
3MGP Binding of Cobalt ions to the Nucleosome Core Particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded CL CHLORIDE ION × 4 CO COBALT (II) ION × 43 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 2.44 Å R-free 0.282
3MGQ Binding of Nickel ions to the Nucleosome Core Particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded NI NICKEL (II) ION × 47 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 2.65 Å R-free 0.276
3MGR Binding of Rubidium ions to the Nucleosome Core Particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded CL CHLORIDE ION × 4 RB RUBIDIUM ION × 5 MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 2.30 Å R-free 0.267
3MGS Binding of Cesium ions to the Nucleosome Core particle Deposited 2010-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded CL CHLORIDE ION × 4 CS CESIUM ION × 12 MN MANGANESE (II) ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
Resolution 3.15 Å R-free 0.238
3MNN A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core Deposited 2010-04-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RU RUTHENIUM ION × 3 MML 1-methyl-4-(1-methylethyl)benzene × 3 PTW 1,3,5-triaza-7-phosphatricyclo[3.3.1.1~3,7~]decane × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；55mM KCl, 85mM MnCl2, 20mM K-Cacodylate, pH 6, VAPOR DIFFUSION, temperature 291K
Resolution 2.50 Å R-free 0.277
3MVD Crystal structure of the chromatin factor RCC1 in complex with the nucleosome core particle Deposited 2010-05-04 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；294 K；25 mM sodium acetate buffer, 25 mM sodium citrate, 1 mM DTT, 6 % PEG2000-MME, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 2.90 Å R-free 0.215
3O62 Nucleosome core particle modified with a cisplatin 1,3-cis-{Pt(NH3)2}2+-d(GpTpG) intrastrand cross-link Deposited 2010-07-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded CPT Cisplatin × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；40-46 mM MnCl2, 30-45 mM KCl, and 20 mM potassium cacodylate pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.22 Å R-free 0.306
3REH 2.5 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Deposited 2011-04-04 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 D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；KCl, MnCl2, K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.50 Å R-free 0.270
3REI 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride Deposited 2011-04-04 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 D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded PT PLATINUM (II) ION × 49 SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.65 Å R-free 0.276
3REJ 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Deposited 2011-04-04 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 D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded MN MANGANESE (II) ION × 13 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.55 Å R-free 0.262
3REK 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Oxaliplatin Deposited 2011-04-04 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 D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded MN MANGANESE (II) ION × 2 PT PLATINUM (II) ION × 40 SO4 SULFATE ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å R-free 0.281
3REL 2.7 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Triamminechloroplatinum(II) Chloride Deposited 2011-04-04 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 D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded MN MANGANESE (II) ION × 2 PT PLATINUM (II) ION × 48 SO4 SULFATE ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.302
3TU4 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Deposited 2011-09-15 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.241
3TU4 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Deposited 2011-09-15 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 3.00 Å R-free 0.241
3UT9 Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601' Derivative (NCP-601L) Deposited 2011-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 29 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.20 Å R-free 0.289
3UTA Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence Containing Two TTAAA elements (NCP-TA2) Deposited 2011-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.07 Å R-free 0.266
3UTB Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite Sequence (NCP146b) Deposited 2011-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded MN MANGANESE (II) ION × 21 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.20 Å R-free 0.275
4J8U X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)osmium(II) Deposited 2013-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded SO4 SULFATE ION × 3 ELJ chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)osmium(II) × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.38 Å R-free 0.280
4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain D 2–126（125 aa）
Not recorded SO4 SULFATE ION × 1 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.58 Å R-free 0.273
4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain H 2–126（125 aa）
Not recorded SO4 SULFATE ION × 2 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.58 Å R-free 0.273
4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded SO4 SULFATE ION × 3 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.58 Å R-free 0.273
4J8W X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) Deposited 2013-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded SO4 SULFATE ION × 3 1MK chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.41 Å R-free 0.275
4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain D 2–126（125 aa）
Not recorded SO4 SULFATE ION × 1 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.87 Å R-free 0.280
4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain H 2–126（125 aa）
Not recorded SO4 SULFATE ION × 2 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.87 Å R-free 0.280
4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded SO4 SULFATE ION × 3 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.87 Å R-free 0.280
4KGC Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM Deposited 2013-04-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded HRU (ethane-1,2-diamine-kappa~2~N,N')[(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)cyclohexane-1,2,3,4,5,6-hexayl]ruthenium × 4 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.69 Å R-free 0.282
4KHA Structural basis of histone H2A-H2B recognition by the essential chaperone FACT Deposited 2013-04-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 34–126（93 aa） Fragment：UNP residues 652-945 and 34-126
Not recorded CL CHLORIDE ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；manual setup 1ul protein (15 mg / ml) plus 1 ul crystallization buffer (7.25% [vol/vol] PEG8000, 0.2 M MgCl2, 0.1 M Tris pH 7.8), VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.35 Å R-free 0.229
4LD9 Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle Deposited 2013-06-24 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293.15 K；50 mM MES pH 6.5, 12% PEG 400, 12 mM MnCl2, 100 mM NaCl, 10 mM EDTA, VAPOR DIFFUSION, temperature 293.15K
Resolution 3.31 Å R-free 0.295
4R8P Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle Deposited 2014-09-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions Modified micro batch under oil；pH 7.5；294 K；25 mM HEPES pH 7.5, 80 mM NH4NO3, 3 % PEG2000-MME, Modified micro batch under oil, temperature 294K
Resolution 3.28 Å R-free 0.245
4WU8 Structure of trPtNAP-NCP145 Deposited 2014-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Mutation：S29T Mutation：S29T CX3 [2-(3-{bis[2-(amino-kappaN)ethyl]amino-kappaN}propyl)-1H-benzo[de]isoquinoline-1,3(2H)-dionato(2-)]platinum(1+) × 2 SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.45 Å R-free 0.263
4WU9 Structure of cisPtNAP-NCP145 Deposited 2014-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Mutation：S29T Mutation：S29T SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 CX8 [2-{3-[(2-{[2-(amino-kappaN)ethyl]amino-kappaN}ethyl)amino-kappaN]propyl}-1H-benzo[de]isoquinoline-1,3(2H)-dionato(3-)]platinum × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Manganese chloride, potassium chloride, potassium cacodylate
Resolution 2.60 Å R-free 0.273
4XUJ Nucleosome core particle containing adducts from treatment with a thiomorpholine-substituted [(eta-6-p-cymene)Ru(3-hydroxy-2-pyridone)Cl] compound Deposited 2015-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa） Fragment：UNP residues 2-126
Chain H 2–126（125 aa） Fragment：UNP residues 2-126
Not recorded SO4 SULFATE ION × 3 4A6 [(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)benzene]ruthenium × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40mM MnCl2, 30mM KCl, 20mM K-Cacodylate
Resolution 3.18 Å R-free 0.299
4XZQ Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-02-04 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 34–126（93 aa） Fragment：residues 34-126
Chain H 34–126（93 aa） Fragment：residues 34-126
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292.15 K；potassium chloride, potassium cacodylate, manganese chloride
Resolution 2.40 Å R-free 0.299
4YS3 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-03-16 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 34–126（93 aa） Fragment：residues 34-126
Chain H 34–126（93 aa） Fragment：residues 34-126
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；292.15 K；postassium chloride, manganese chloride, cacodylate
Resolution 3.00 Å R-free 0.279
4Z66 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-04-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 33–126（94 aa）
Chain H 33–126（94 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292.15 K；potassium chloride, potassium cacodylate, manganese chloride
Resolution 2.50 Å R-free 0.296
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
Resolution 3.82 Å R-free 0.256
4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric
Chain N 5–126（122 aa）
Chain R 5–126（122 aa）
Not recorded ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
Resolution 3.82 Å R-free 0.256
5CP6 Nucleosome Core Particle with Adducts from the Anticancer Compound, [(eta6-5,8,9,10-tetrahydroanthracene)Ru(ethylenediamine)Cl][PF6] Deposited 2015-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded RUH (ethane6-5,8,9,10-tetrahydroanthracene)Ru(II)(ethylene-diamine)Cl × 3 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.251
5DNM Nucleosome core particle containing adducts of ruthenium(II)-toluene PTA complex Deposited 2015-09-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RAX dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate
Resolution 2.81 Å R-free 0.241
5DNN Nucleosome core particle containing adducts of gold(I)-triethylphosphane and ruthenium(II)-toluene PTA complexes Deposited 2015-09-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded AUF triethylphosphanuidylgold(1+) × 2 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RAX dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate
Resolution 2.80 Å R-free 0.236
5E5A Crystal structure of the chromatin-tethering domain of Human cytomegalovirus IE1 protein bound to the nucleosome core particle Deposited 2015-10-08 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 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；289 K；sodium cacodylate, magnesium acetate, 2-methyl-2,4-pentanediol
Resolution 2.81 Å R-free 0.242
5F99 X-ray Structure of the MMTV-A Nucleosome Core Particle Deposited 2015-12-09 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 D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded CL CHLORIDE ION × 4 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；sample was mixed 1:1 with 10 mM K-cacodylate, pH 6.0, 180 mM MgCl2, 50 mM KCl and equilibrated against a 1:4 dilution of the same solution
Resolution 2.63 Å R-free 0.252
5G2E Structure of the Nap1 H2A H2B complex Deposited 2016-04-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 28–126（99 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 10-15% W/V PEG3350; 200 MM LICL
Resolution 6.70 Å R-free 0.310
5G2E Structure of the Nap1 H2A H2B complex Deposited 2016-04-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 28–126（99 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 10-15% W/V PEG3350; 200 MM LICL
Resolution 6.70 Å R-free 0.310
5G2E Structure of the Nap1 H2A H2B complex Deposited 2016-04-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 28–126（99 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 10-15% W/V PEG3350; 200 MM LICL
Resolution 6.70 Å R-free 0.310
5G2E Structure of the Nap1 H2A H2B complex Deposited 2016-04-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain T 28–126（99 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 10-15% W/V PEG3350; 200 MM LICL
Resolution 6.70 Å R-free 0.310
5G2E Structure of the Nap1 H2A H2B complex Deposited 2016-04-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain X 28–126（99 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 10-15% W/V PEG3350; 200 MM LICL
Resolution 6.70 Å R-free 0.310
5G2E Structure of the Nap1 H2A H2B complex Deposited 2016-04-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain P 28–126（99 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 10-15% W/V PEG3350; 200 MM LICL
Resolution 6.70 Å R-free 0.310
5HQ2 Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle Deposited 2016-01-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: hexadecameric
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 5.5；277 K；25 mM sodium acetate pH 5.5, 40 mM sodium citrate,1 mM DTT, 6% PEG2000-MME
Resolution 4.50 Å R-free 0.397
5NL0 Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1 Deposited 2017-04-03 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293.15 K；Mix of equal volumes of the nucleosome/H1 complex (25-30 microM) and a crystallization solution composed of MPD (6% v/v), 50 mM NaCl, and 50 mM sodium potassium phosphate pH 6.4.
Resolution 5.40 Å R-free 0.265
5NL0 Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1 Deposited 2017-04-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain N 5–126（122 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293.15 K；Mix of equal volumes of the nucleosome/H1 complex (25-30 microM) and a crystallization solution composed of MPD (6% v/v), 50 mM NaCl, and 50 mM sodium potassium phosphate pH 6.4.
Resolution 5.40 Å R-free 0.265
5O9G Structure of nucleosome-Chd1 complex Deposited 2017-06-19 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–125（121 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
5OMX X-ray Structure of the H2A-N38C Nucleosome Core Particle Deposited 2017-08-02 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 D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded MN MANGANESE (II) ION × 33 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；8 mg/ml sample was mixed 1:1 with 10 mM K-Cacodylate (pH 6.0), 140-150 mM MnCl2, 100 KCl. and equilibrated against a 1:4 dilution of the same solution
Resolution 2.32 Å R-free 0.259
5ONG X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer Deposited 2017-08-03 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 D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded MN MANGANESE (II) ION × 20 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；Sample was mixed in a 1:1 ratio with 10 mM Na-cacodylate, pH 6.0, 130-180 mM MnCl2, 100-160 mM KCl and equilibrated against a 1:4 dilution of the same solution
Resolution 2.80 Å R-free 0.247
5ONW X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two H2A/H2B dimers crosslinked via H2A N38C Deposited 2017-08-04 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 D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded MN MANGANESE (II) ION × 20 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；Sample was mixed in a 1:1 ratio with 10 mM Na-cacodylate, pH 6.0, 160-210 mM MnCl2, 140-200 mM KCl and equilibrated against a 1:4 dilution of the same solution
Resolution 2.80 Å R-free 0.254
5OXV Structure of the 4_601_157 tetranucleosome (C2 form) Deposited 2017-09-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；291 K；30-60 mM KCl, 90-110 mM MgCl2 and 5 mM Na-cacodylate, pH 6
Resolution 6.72 Å R-free 0.352
5OY7 Structure of the 4_601_157 tetranucleosome (P1 form) Deposited 2017-09-07 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 × 32 PDB declaration: 34-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain L 1–126（126 aa）
Chain P 1–126（126 aa）
Chain T 1–126（126 aa）
Chain X 1–126（126 aa）
Chain b 1–126（126 aa）
Chain f 1–126（126 aa）
Not recorded CL CHLORIDE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；30-60 mM KCl, 90-110 mM MgCl2 and 5 mM Na-cacodyalte, pH 6.0
Resolution 5.77 Å R-free 0.238
5X0X Complex of Snf2-Nucleosome complex with Snf2 bound to position +6 of the nucleosome Deposited 2017-01-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
5X0Y Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome Deposited 2017-01-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.69 Å
5XF6 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker Deposited 2017-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 EDN ETHANE-1,2-DIAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0
Resolution 2.63 Å R-free 0.254
5Z3L Structure of Snf2-nucleosome complex in apo state Deposited 2018-01-08 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.31 Å
5Z3O Structure of Snf2-nucleosome complex in ADP state Deposited 2018-01-08 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
5Z3U Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state Deposited 2018-01-08 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.31 Å
5Z3V Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state Deposited 2018-01-08 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.22 Å
6ESF Nucleosome : Class 1 Deposited 2017-10-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ESG Nucleosome breathing : Class 2 Deposited 2017-10-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.40 Å
6ESH Nucleosome breathing : Class 3 Deposited 2017-10-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
6ESI Nucleosome breathing : Class 4 Deposited 2017-10-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
6I84 Structure of transcribing RNA polymerase II-nucleosome complex Deposited 2018-11-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain R 5–126（122 aa）
Chain W 5–126（122 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6IRO the crosslinked complex of ISWI-nucleosome in the ADP-bound state Deposited 2018-11-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6J99 Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome Deposited 2019-01-22 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T, K117C Mutation：S29T, K117C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6JM9 cryo-EM structure of DOT1L bound to unmodified nucleosome Deposited 2019-03-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 34–126（93 aa）
Chain H 34–126（93 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.30 Å
6JMA cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome Deposited 2019-03-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 34–126（93 aa）
Chain H 34–126（93 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
6JYL The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state Deposited 2019-04-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE；blot 1.5s
Resolution 3.37 Å
6K01 Crystal structure of xH2A-H2B Deposited 2019-05-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 28–126（99 aa）
Mutation：S30T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Ammonium sulfate, 0.1M HEPES pH=7.5, 25% PEG 3350
Resolution 2.84 Å R-free 0.278
6K1P The complex of ISWI-nucleosome in the ADP.BeF-bound state Deposited 2019-05-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5；10 mM Tris, 50 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE；blot for 1.5s
Resolution 3.87 Å
6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T/K117T Mutation：S29T/K117T SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T/K117C Mutation：S29T/K117C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIW Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T/K117C Mutation：S29T/K117C ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIX Cryo-EM structure of human MLL1-NCP complex, binding mode1 Deposited 2019-07-20 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T/K117C Mutation：S29T/K117C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6KIZ Cryo-EM structure of human MLL1-NCP complex, binding mode2 Deposited 2019-07-20 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T/K117C Mutation：S29T/K117C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6N1Z Importin-9 bound to H2A-H2B Deposited 2018-11-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 5–126（122 aa） Fragment：HISTONE H2B 1.1
Mutation：S33T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.04 M MES, 0.11 M potassium acetate, 2 mM magnesium acetate, 2 mM DTT, 3.0 M potassium formate, 25% glycerol
Resolution 2.70 Å R-free 0.238
6N1Z Importin-9 bound to H2A-H2B Deposited 2018-11-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 5–126（122 aa） Fragment：HISTONE H2B 1.1
Mutation：S33T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.04 M MES, 0.11 M potassium acetate, 2 mM magnesium acetate, 2 mM DTT, 3.0 M potassium formate, 25% glycerol
Resolution 2.70 Å R-free 0.238
6NJ9 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex Deposited 2019-01-02 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S32T, K120C Mutation：S32T, K120C SAM S-ADENOSYLMETHIONINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing.
Resolution 2.96 Å
6NN6 Structure of Dot1L-H2BK120ub nucleosome complex Deposited 2019-01-14 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S33T, K121C Mutation：S33T, K121C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6NOG Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome Deposited 2019-01-16 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S32T, K120C Mutation：S32T, K120C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing
Resolution 3.90 Å
6NQA Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex Deposited 2019-01-19 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S32T, K120C Mutation：S32T, K120C SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing.
Resolution 3.54 Å
6NZO Set2 bound to nucleosome Deposited 2019-02-14 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T Mutation：S29T ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6O96 Dot1L bound to the H2BK120 Ubiquitinated nucleosome Deposited 2019-03-13 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：K120C, S32T Mutation：K120C, S32T SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen PROPANE；blotted for 3s before plunging
Resolution 3.50 Å
6OM3 Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle Deposited 2019-04-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Mutation：S32T Mutation：S32T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277.15 K；6 mM Na-Cacodylate pH 6.0, 0.4 mM Spermine-HCl, 2 mM MgCl2 and 1.75% v/v PEG 400
Resolution 3.30 Å R-free 0.250
6OM3 Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle Deposited 2019-04-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain P 1–126（126 aa）
Chain T 1–126（126 aa）
Mutation：S32T Mutation：S32T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277.15 K；6 mM Na-Cacodylate pH 6.0, 0.4 mM Spermine-HCl, 2 mM MgCl2 and 1.75% v/v PEG 400
Resolution 3.30 Å R-free 0.250
6PA7 The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. Deposited 2019-06-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded CL CHLORIDE ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain J 5–126（122 aa）
Chain N 5–126（122 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
6PWW Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain J 5–126（122 aa）
Chain N 5–126（122 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6PWX Cryo-EM structure of RbBP5 bound to the nucleosome Deposited 2019-07-23 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain J 5–126（122 aa）
Chain N 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6PX1 Set2 bound to nucleosome Deposited 2019-07-24 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T Mutation：S29T No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6PX3 Set2 bound to nucleosome Deposited 2019-07-24 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T Mutation：S29T ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6R1U Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2 Deposited 2019-03-15 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.36 Å
6RYR Nucleosome-CHD4 complex structure (single CHD4 copy) Deposited 2019-06-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6RYU Nucleosome-CHD4 complex structure (two CHD4 copies) Deposited 2019-06-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6S01 Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome Deposited 2019-06-13 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.20 Å
6T9L SAGA DUB module bound to a ubiqitinated nucleosome Deposited 2019-10-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain D 5–126（122 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.60 Å
6TDA Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome Deposited 2019-11-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.00 Å
6TEM CENP-A nucleosome core particle with 145 base pairs of the Widom 601 sequence by cryo-EM Deposited 2019-11-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å
6UGM Structural basis of COMPASS eCM recognition of an unmodified nucleosome Deposited 2019-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain H 2–126（125 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6UXW SWI/SNF nucleosome complex with ADP-BeFx Deposited 2019-11-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain U 5–126（122 aa）
Chain Y 5–126（122 aa）
Not recorded PO4 PHOSPHATE ION × 12 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；10 mM HEPES, pH 7.9, 10 mM MgCl2, 50 mM KCl, 1 mM DTT, 5% glycerol, 0.05% NP-40
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.96 Å
6VEN Yeast COMPASS in complex with a ubiquitinated nucleosome Deposited 2020-01-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：K120C, S30T Mutation：K120C, S30T ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；blot force 5 3.5 sec blot time
Resolution 3.37 Å
6VYP Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate Deposited 2020-02-27 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S32T Mutation：S32T FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 7.5；277 K；25 mM HEPES pH7.5, 75 mM triammonium citrate, 10% PEG2000-MME, Modified Microbatch under oil
Resolution 4.99 Å R-free 0.277
6VYP Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate Deposited 2020-02-27 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain d 5–126（122 aa）
Chain h 5–126（122 aa）
Mutation：S32T Mutation：S32T FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICROBATCH；pH 7.5；277 K；25 mM HEPES pH7.5, 75 mM triammonium citrate, 10% PEG2000-MME, Modified Microbatch under oil
Resolution 4.99 Å R-free 0.277
6W4L The crystal structure of a single chain H2B-H2A histone chimera from Xenopus laevis Deposited 2020-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 34–126（93 aa）
Not recorded PPV PYROPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；291 K；0.2M sodium thiocyanate, 20% PEG3350
Resolution 1.31 Å R-free 0.206
6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain J 5–126（122 aa）
Chain N 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6W5N Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Deposited 2020-03-13 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain J 5–126（122 aa）
Chain N 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
6WKR PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome Deposited 2020-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: octadecameric
Chain M 1–126（126 aa）
Chain S 1–126（126 aa）
Not recorded MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6WZ5 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-13 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
6WZ9 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-13 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6X0N Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-16 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 23-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Chain d 5–126（122 aa）
Chain h 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 10.00 Å
6ZHX Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: nucleosome class. Deposited 2020-06-24 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot time 2.5 s, blot force 0. Two sample applications and blots were performed before vitrification.
Resolution 2.50 Å
6ZHY Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: hexasome class. Deposited 2020-06-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric
Chain D 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot time 2.5 s, blot force 0. Two sample applications and blots were performed before vitrification.
Resolution 3.00 Å
7AT8 Histone H3 recognition by nucleosome-bound PRC2 subunit EZH2. Deposited 2020-10-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain G 5–126（122 aa）
Chain K 5–126（122 aa）
Not recorded ZN ZINC ION × 7 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.40 Å
7E8I Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin Deposited 2021-03-01 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 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
7EG6 Snf5 Finger Helix bound to the nucleosome Deposited 2021-03-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 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
7EGP The structure of SWI/SNF-nucleosome complex Deposited 2021-03-24 Different oligomeric state Different ligand/ion Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain R 5–126（122 aa）
Chain V 5–126（122 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
7ENN The structure of ALC1 bound to the nucleosome Deposited 2021-04-18 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7K6P Active state Dot1 bound to the unacetylated H4 nucleosome Deposited 2020-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 33–125（93 aa）
Chain H 33–125（93 aa）
Mutation：K120C,S32T Mutation：K120C,S32T SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7K6Q Active state Dot1 bound to the H4K16ac nucleosome Deposited 2020-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 33–125（93 aa）
Chain H 33–125（93 aa）
Mutation：K120C, S32T Mutation：K120C, S32T SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7KBD Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction) Deposited 2020-10-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
7KBE Nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction) Deposited 2020-10-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7KBF H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction) Deposited 2020-10-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.42 Å
7M1X Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z Deposited 2021-03-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4.5 seconds before plunging
Resolution 3.70 Å
7MBM Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Deposited 2021-04-01 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain J 5–126（122 aa）
Chain N 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.76 Å
7MBN Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Deposited 2021-04-01 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain J 5–126（122 aa）
Chain N 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.02 Å
7NKX RNA polymerase II-Spt4/5-nucleosome-Chd1 structure Deposited 2021-02-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain d 5–126（122 aa）
Chain h 5–126（122 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7NKY RNA Polymerase II-Spt4/5-nucleosome-FACT structure Deposited 2021-02-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 27-meric
Chain d 5–126（122 aa）
Chain h 5–126（122 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7OH9 Nucleosome with TBP and TFIIA bound at SHL -6 Deposited 2021-05-09 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7OHA nucleosome with TBP and TFIIA bound at SHL +2 Deposited 2021-05-09 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7OHB TBP-nucleosome complex Deposited 2021-05-10 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OHC Cryo-EM structure of nucleosome core particle composed of the Widom 601 DNA sequence Deposited 2021-05-10 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7OTQ Cryo-EM structure of ALC1/CHD1L bound to a PARylated nucleosome Deposited 2021-06-10 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 uL were applied on grid and immediately blotted for 2.5 s at blot force 0.
Resolution 4.80 Å
7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S32T, K120C Mutation：S32T, K120C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
7UNC Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome Deposited 2022-04-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 29 PDB declaration: 32-meric
Chain d 5–126（122 aa）
Chain h 5–126（122 aa）
Mutation：S29T Mutation：S29T ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7UND Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) Deposited 2022-04-10 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain d 5–126（122 aa）
Chain h 5–126（122 aa）
Mutation：S29T Mutation：S29T ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7VDT The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7VDV The overall structure of human chromatin remodeling PBAF-nucleosome complex Deposited 2021-09-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7VVU NuA4 HAT module bound to the nucleosome Deposited 2021-11-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain D 1–126（126 aa）
Chain U 1–126（126 aa）
Not recorded CMC CARBOXYMETHYL COENZYME *A × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.40 Å
7VVZ NuA4 bound to the nucleosome Deposited 2021-11-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain D 1–126（126 aa）
Chain U 1–126（126 aa）
Not recorded CMC CARBOXYMETHYL COENZYME *A × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.80 Å
7X3T Cryo-EM structure of ISW1a-dinucleosome Deposited 2022-03-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Chain N 1–126（126 aa）
Chain R 1–126（126 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.40 Å
7X3V Cryo-EM structure of IOC3-N2 nucleosome Deposited 2022-03-01 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
7X3W Cryo-EM structure of ISW1-N1 nucleosome Deposited 2022-03-01 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7X3X Cryo-EM structure of N1 nucleosome-RA Deposited 2022-03-01 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7XFC Structure of nucleosome-DI complex (-30I, Apo state) Deposited 2022-04-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.90 Å
7XFH Structure of nucleosome-AAG complex (A-30I, post-catalytic state) Deposited 2022-04-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.90 Å
7XFI Structure of nucleosome-DI complex (-50I, Apo state) Deposited 2022-04-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.90 Å
7XFJ Structure of nucleosome-AAG complex (T-50I, post-catalytic state) Deposited 2022-04-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.00 Å
7XFL Structure of nucleosome-AAG complex (A-53I, free state) Deposited 2022-04-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.80 Å
7XFM Structure of nucleosome-AAG complex (A-53I, post-catalytic state) Deposited 2022-04-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.10 Å
7XFN Structure of nucleosome-DI complex (-55I, Apo state) Deposited 2022-04-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.80 Å
7XNP Structure of nucleosome-AAG complex (A-55I, post-catalytic state) Deposited 2022-04-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.90 Å
7XPX Cryo-EM structure of the histone methyltransferase SET8 bound to H4K20Ecx-nucleosome Deposited 2022-05-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7YI1 Cryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome Deposited 2022-07-14 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T Mutation：S29T No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7YI4 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in close state Deposited 2022-07-14 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain J 5–126（122 aa）
Chain N 5–126（122 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
7YI5 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in loose state Deposited 2022-07-14 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain J 5–126（122 aa）
Chain N 5–126（122 aa）
Mutation：S29T Mutation：S29T ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
7YRD histone methyltransferase Deposited 2022-08-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Not recorded ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7YRG histone methyltransferase Deposited 2022-08-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 32–126（95 aa）
Chain H 32–126（95 aa）
Mutation：S33T Mutation：S33T ZN ZINC ION × 2 SAM S-ADENOSYLMETHIONINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain d 2–126（125 aa）
Chain h 2–126（125 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain d 2–126（125 aa）
Chain h 2–126（125 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain d 2–126（125 aa）
Chain h 2–126（125 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
8B0A Cryo-EM structure of ALC1 bound to an asymmetric, site-specifically PARylated nucleosome Deposited 2022-09-07 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8BZ1 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Deposited 2022-12-14 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain d 1–126（126 aa）
Chain h 1–126（126 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 3.80 Å
8CBN structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Deposited 2023-01-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
8CBQ structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Deposited 2023-01-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8DU4 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Deposited 2022-07-26 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S32T, K120C Mutation：S32T, K120C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
8ETT Class1 of the INO80-Hexasome complex Deposited 2022-10-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain D 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 6.68 Å
8ETV Class2 of the INO80-Hexasome complex Deposited 2022-10-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain D 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.16 Å
8EU2 Class3 of the INO80-Hexasome complex Deposited 2022-10-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain D 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 2.93 Å
8F86 SIRT6 bound to an H3K9Ac nucleosome Deposited 2022-11-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ZSL [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3aR,5R,6R,6aR)-6-hydroxytetrahydro-2H-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8G6G H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 5 Deposited 2023-02-15 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S33T, K120C Mutation：S33T, K120C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
8G6H H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 6 Deposited 2023-02-15 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S33T, K120C Mutation：S33T, K120C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
8G6Q H2AK119ub-modified nucleosome ubiquitin position 1 Deposited 2023-02-15 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S33T Mutation：S33T No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.41 Å
8G6S H2AK119ub-modified nucleosome ubiquitin position 2 Deposited 2023-02-15 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S33T Mutation：S33T No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
8G86 Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of nucleosome) Deposited 2023-02-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
8G88 Human Oct4 bound to nucleosome with human nMatn1 sequence Deposited 2023-02-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
8G8B Nucleosome with human nMatn1 sequence in complex with Human Oct4 Deposited 2023-02-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
8G8G Interaction of H3 tail in LIN28B nucleosome with Oct4 Deposited 2023-02-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8GPN Human menin in complex with H3K79Me2 nucleosome Deposited 2022-08-26 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8KD2 Rpd3S in complex with 187bp nucleosome Deposited 2023-08-09 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain R 5–126（122 aa）
Chain V 5–126（122 aa）
Mutation：S29T Mutation：S29T No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8KD3 Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA Deposited 2023-08-09 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain R 5–126（122 aa）
Chain V 5–126（122 aa）
Mutation：S29T Mutation：S29T ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8KD4 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1 Deposited 2023-08-09 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain R 5–126（122 aa）
Chain V 5–126（122 aa）
Mutation：S29T Mutation：S29T ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
8KD5 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2 Deposited 2023-08-09 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain R 5–126（122 aa）
Chain V 5–126（122 aa）
Mutation：S29T Mutation：S29T ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8KD6 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3 Deposited 2023-08-09 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain R 5–126（122 aa）
Chain V 5–126（122 aa）
Mutation：S29T Mutation：S29T ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
8KD7 Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA Deposited 2023-08-09 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric
Chain R 5–126（122 aa）
Chain V 5–126（122 aa）
Mutation：S29T Mutation：S29T No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
8PC5 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex Deposited 2023-06-09 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
8PC6 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Deposited 2023-06-09 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8PEO H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex Deposited 2023-06-14 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
8PEP H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Deposited 2023-06-14 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
8RUP Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome Deposited 2024-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；3 s blotting time, -10 force, no wait time.
Resolution 2.42 Å
8RUQ Borealin N-terminus in complex with H3.T3p-nucleosome Deposited 2024-01-31 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside
cryo-EM vitrification conditions Cryogen ETHANE；3 s blotting time, -10 force, no wait time.
Resolution 2.29 Å
8SIY Origin Recognition Complex Associated (ORCA) protein bound to H4K20me3-nucleosome Deposited 2023-04-17 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain F 5–126（122 aa）
Chain J 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8SKZ Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome Deposited 2023-04-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8SVF BAP1/ASXL1 bound to the H2AK119Ub Nucleosome Deposited 2023-05-16 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Mutation：S33T Mutation：S33T No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8T3T Structure of Bre1-nucleosome complex - state3 Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.21 Å
8T3W Structure of Bre1-nucleosome complex - state2 Deposited 2023-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
8T3Y Structure of Bre1-nucleosome complex - state1 Deposited 2023-06-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES, pH 7.5, 50 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
8T9F Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Deposited 2023-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8T9G Automethylated PRC2 dimer bound to nucleosome Deposited 2023-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain S 5–126（122 aa）
Chain V 5–126（122 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.20 Å
8T9H Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Deposited 2023-06-24 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
8TAS PRC2 monomer bound to nucleosome Deposited 2023-06-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain S 5–126（122 aa）
Chain V 5–126（122 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8TB9 PRC2-J119-450 monomer bound to H1-nucleosome Deposited 2023-06-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain S 5–126（122 aa）
Chain V 5–126（122 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8THU Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Deposited 2023-07-18 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8TOF Rpd3S bound to an H3K36Cme3 modified nucleosome Deposited 2023-08-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric
Chain d 5–126（122 aa）
Chain h 5–126（122 aa）
Mutation：S29T Mutation：S29T ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8U5H Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome Deposited 2023-09-12 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 5–126（122 aa）
Chain S 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
8UW1 Cryo-EM structure of DNMT3A1 UDR in complex with H2AK119Ub-nucleosome Deposited 2023-11-05 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8UXQ Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome Deposited 2023-11-09 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain H 2–126（125 aa）
Chain N 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
8V25 H2BK120ub-modified nucleosome ubiquitin position 1 Deposited 2023-11-21 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T, K117C Mutation：S29T, K117C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
8V26 H2BK120ub-modified nucleosome ubiquitin position 2 Deposited 2023-11-21 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T, K117C Mutation：S29T, K117C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
8V27 H2BK120ub-modified nucleosome ubiquitin position 3 Deposited 2023-11-21 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T, K117C Mutation：S29T, K117C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
8V28 H2BK120ub-modified nucleosome ubiquitin position 4 Deposited 2023-11-22 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T, K117C Mutation：S29T, K117C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
8V4Y Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 1) Deposited 2023-11-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T Mutation：S29T ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8V6V Cryo-EM structure of doubly-bound SNF2h-nucleosome complex Deposited 2023-12-03 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T Mutation：S29T ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8V7L Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 2) Deposited 2023-12-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T Mutation：S29T ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8VO0 H3K36me3-modified nucleosome bound to PRC2_AJ1-450 with histone H3 tail disengaged Deposited 2024-01-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 40–126（87 aa）
Chain S 38–126（89 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8VOB H3K36me3-modified nucleosome bound to PRC2_AJ1-450 Deposited 2024-01-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain M 31–126（96 aa）
Chain S 31–126（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VX5 Nucleosome core particle containing an 8-oxoG damage site Deposited 2024-02-03 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T Mutation：S29T No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8VX6 Human OGG1 bound at the nucleosomal DNA entry site Deposited 2024-02-03 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S29T Mutation：S29T No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8XAA Structure of NAP1 in complex with H2A-H2B Deposited 2023-12-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain J 28–126（99 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris, pH 8.0, 25 % v/v PEG 400
Resolution 3.35 Å R-free 0.261
8XAA Structure of NAP1 in complex with H2A-H2B Deposited 2023-12-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain L 28–126（99 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris, pH 8.0, 25 % v/v PEG 400
Resolution 3.35 Å R-free 0.261
8XJV Structural basis for the linker histone H5-nucleosome binding and chromatin compaction Deposited 2023-12-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 108 PDB declaration: 110-meric
Chain Aa 5–126（122 aa）
Chain Ab 5–126（122 aa）
Chain Ac 5–126（122 aa）
Chain Ad 5–126（122 aa）
Chain Af 5–126（122 aa）
Chain Ag 5–126（122 aa）
Chain At 5–126（122 aa）
Chain J 5–126（122 aa）
Chain M 5–126（122 aa）
Chain N 5–126（122 aa）
Chain O 5–126（122 aa）
Chain P 5–126（122 aa）
Chain Q 5–126（122 aa）
Chain R 5–126（122 aa）
Chain S 5–126（122 aa）
Chain T 5–126（122 aa）
Chain U 5–126（122 aa）
Chain V 5–126（122 aa）
Chain W 5–126（122 aa）
Chain av 5–126（122 aa）
Chain aw 5–126（122 aa）
Chain ax 5–126（122 aa）
Chain ay 5–126（122 aa）
Chain az 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.60 Å
8ZVY Alpha-Synuclein with H2a-H2b dimer complex structure. Deposited 2024-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 34–126（93 aa）
Chain B 34–126（93 aa）
Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291.15 K；100 mM Tris pH 8.0 and 10% PEG 8000.
Resolution 1.72 Å R-free 0.220
9B2S Haspin bound to nucleosome in position 1 Deposited 2024-03-16 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S33T Mutation：S33T No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
9B2T Haspin bound to nucleosome in position 2 Deposited 2024-03-16 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S33T Mutation：S33T No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å
9B3P The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome Deposited 2024-03-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；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
9C9X S.c INO80 in complex with Xenopus 0/80 nucleosome, Nucleosome Deposited 2024-06-16 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 2.83 Å
9CA7 Cryo-EM structure of human SRCAP-nucleosome complex in the fully-engaged state (composite structure) Deposited 2024-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain R 2–126（125 aa）
Chain T 2–126（125 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 5 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
9CA8 Cryo-EM structure of human SRCAP-nucleosome complex in the partially-engaged state (composite structure) Deposited 2024-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain R 2–126（125 aa）
Chain T 2–126（125 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 5 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
9CAA Cryo-EM structure of human SRCAP-nucleosome complex in the pre-engaged state (composite structure) Deposited 2024-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain R 2–126（125 aa）
Chain T 2–126（125 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.04 Å
9CAB Cryo-EM structure of human SRCAP-nucleosome complex in the encounter state (composite structure) Deposited 2024-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain R 2–126（125 aa）
Chain T 2–126（125 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 5 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.94 Å
9CAN S.c INO80 in complex with Xenopus 0/40 nucleosome Deposited 2024-06-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen OTHER
Resolution 3.30 Å
9CG9 Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2 Deposited 2024-06-28 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Mutation：S32T Mutation：S32T No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 uL of sample was applied to grid.
Resolution 2.94 Å
9DBY ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome Deposited 2024-08-24 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Mutation：S33T Mutation：S33T ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9DDE ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome Deposited 2024-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Mutation：S33T Mutation：S33T ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9DG3 ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome Deposited 2024-09-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Mutation：S33T Mutation：S33T ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9DGG ncPRC1RYBP bound to unmodified nucleosome Deposited 2024-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Mutation：S33T Mutation：S33T ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9E1L Snf2h bound nucleosome complex - ClassA1 Deposited 2024-10-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
9E1M Snf2h bound nucleosome complex - ClassA2 Deposited 2024-10-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
9E1N Snf2h bound nucleosome complex-ClassA3 Deposited 2024-10-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9E1O Snf2h bound nucleosome complex - ClassB1 Deposited 2024-10-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E1P Snf2h bound nucleosome complex - ClassB2 Deposited 2024-10-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
9E1Q Snf2h bound nucleosome complex - ClassB3 Deposited 2024-10-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9E1R Snf2h bound nucleosome complex - ClassB4 Deposited 2024-10-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9E1U Snf2h bound nucleosome complex - ClassC1 Deposited 2024-10-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9E1V Snf2h bound nucleosome complex - ClassC2 Deposited 2024-10-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9E1W Snf2h bound nucleosome complex - ClassC3 Deposited 2024-10-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9E1X Snf2h bound nucleosome complex - ClassD1 Deposited 2024-10-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9E1Y Empty Nucleosome with 601 widom sequence Deposited 2024-10-21 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EGX RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27 Deposited 2024-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 29 PDB declaration: 32-meric
Chain d 5–126（122 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9EGY RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain d 5–126（122 aa）
Chain h 5–126（122 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9EGZ RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain d 5–126（122 aa）
Chain h 5–126（122 aa）
Not recorded ZN ZINC ION × 12 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9EH0 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain d 5–126（122 aa）
Chain h 5–126（122 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9EH1 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain d 5–126（122 aa）
Chain h 5–126（122 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9EH2 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream Deposited 2024-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain h 5–126（122 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9EIL SIRT6 bound to an H3K27Ac nucleosome Deposited 2024-11-26 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ZSL [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3aR,5R,6R,6aR)-6-hydroxytetrahydro-2H-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9F0O The molecular basis and modulation of lamin-specific chromatin interaction Deposited 2024-04-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 30–126（97 aa）
Chain H 30–126（97 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9FH9 Structure of CyclinB1 N-terminus bound to the NCP Deposited 2024-05-27 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9GD0 Structure of a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Chain N 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9GD1 Structure of Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Chain N 5–126（122 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9GD2 Structure of Chd1 bound to a dinucleosome with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Chain N 5–126（122 aa）
Chain Q 5–126（122 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9GD3 Structure of a mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA. Deposited 2024-08-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9GEN Recombinant Myeloperoxidase bound to nucleosome core particle Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 30–125（96 aa）
Chain H 30–125（96 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.76 Å
9GEO Nucleosome core particle Deposited 2024-08-07 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 30–125（96 aa）
Chain H 30–125（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.79 Å
9GEP Native monomeric Myeloperoxidase bound to nucleosome core particle Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain D 30–125（96 aa）
Chain H 30–125（96 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
9GEQ Native dimeric Myeloperoxidase bound to nucleosome core particle; composite map Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain D 30–125（96 aa）
Chain H 30–125（96 aa）
Not recorded CL CHLORIDE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9GER Native dimeric Myeloperoxidase bound to nucleosome core particle, intermediate state; composite map Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain D 30–125（96 aa）
Chain H 30–125（96 aa）
Not recorded CL CHLORIDE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.58 Å
9IGJ structure of two human ELF2 transcription factors in complex with a nucleosome Deposited 2025-02-19 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；1 mM EDTA, 30 mM NaCl, 2 mM DTT in 20 mM HEPES, pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9IHD Nucleosome core particle bound by one molecule of DTT-reduced native monomeric myeloperoxidase Deposited 2025-02-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain D 30–125（96 aa）
Chain H 30–125（96 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
9IHE Nucleosome core particle bound by two molecules of DTT-reduced native monomeric myeloperoxidase Deposited 2025-02-21 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain D 30–125（96 aa）
Chain H 30–125（96 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9IHF Nucleosome core particle bound by one monomer and one dimer of of DTT-reduced native myeloperoxidase Deposited 2025-02-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric
Chain D 30–125（96 aa）
Chain H 30–125（96 aa）
Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9JAO The structure of SMARCAD1 bound to the hexasome in the presence of ADP-BeFx Deposited 2024-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain H 5–126（122 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9M76 UHRF1 bound to a mononucleosome in its pre-active state, with the RING domain bound to the SRA domain. Deposited 2025-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
9M77 The activated state of human UHRF1 bound to a mononucleosome, with the finger loop ordered and linker 4 disordered. Deposited 2025-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9MPP The cryo-EM structure of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L Deposited 2024-12-31 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ZN ZINC ION × 6 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9N6H 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex Deposited 2025-02-05 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 33–126（94 aa）
Chain H 33–126（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.54 Å
9N6I 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex Deposited 2025-02-05 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 33–126（94 aa）
Chain H 33–126（94 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.61 Å
9NH8 CHD1-nucleosome complex (anchored state) Deposited 2025-02-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ARG ARGININE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9NY4 USP21 bound to H2AK119ub nucleosome Deposited 2025-03-26 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9Q7U Composite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer bound to 167H3K36me2-nucleosome Deposited 2025-08-25 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded ZN ZINC ION × 9 SAO 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9QAJ Structure of the nucleosome-bound human BCL7A Deposited 2025-02-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QIK M2 nucleosome Deposited 2025-03-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–126（126 aa）
Chain D 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9R5K Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Hepes, 120mM Nacl
cryo-EM vitrification conditions Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity
Resolution 4.20 Å
9R5S Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-09 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Hepes, 120mM Nacl
cryo-EM vitrification conditions Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity
Resolution 3.80 Å
9R5W Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–126（126 aa）
Chain H 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Hepes, 120mM Nacl
cryo-EM vitrification conditions Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity
Resolution 3.80 Å
9T4V ALC1/CHD1L in an intermediate conformation, bound to a PARylated nucleosome Deposited 2025-11-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3 uL were applied on grid and immediately blotted for 2.5 s at blot force 0.
Resolution 6.60 Å
9W74 Cryo-EM structure of the close-packed di-hexasome (CPDH) Deposited 2025-08-05 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 5–126（122 aa）
Chain N 5–126（122 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.94 Å
9WBZ The structure of NCP-motor-ARP module of ncBAF-nucleosome complex Deposited 2025-08-15 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9WC0 The structure of NCP-RA module of ncBAF-nucleosome complex Deposited 2025-08-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 2–126（125 aa）
Chain H 2–126（125 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
9XYC Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome LEDGF+nucleosome map Q Deposited 2025-08-25 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain d 1–126（126 aa）
Chain h 1–126（126 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9Y4P Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker Deposited 2025-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain D 5–126（122 aa）
Chain H 5–126（122 aa）
Chain P 5–126（122 aa）
Chain T 5–126（122 aa）
Not recorded ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.84 Å

310 other PDB entries and 327 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H2B11_XENLA
Isoform —
PDB entities 8
Chains and sequence ranges Author chain J； PDBConstruct 1–122； UniProt 5–126 Author chain N； PDBConstruct 1–122； UniProt 5–126

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 6w5i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6w5i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6w5i
Deposition date deposition_date2020-03-13
Structure title titleCryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class01)
Keywords keywordsMLL1-NCP, H3K4 methylation, TRANSFERASE, TRANSFERASE-STRUCTURAL PROTEIN-DNA complex; TRANSFERASE/STRUCTURAL PROTEIN/DNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier48.01 Å
Radius of gyration Rg (electron density) rg_electron47.25 Å
Forward intensity I(0) i01721520000.00
Molecular weight molecular_weight284860.0 kDa
Excluded volume excluded_volume331420 ų
Envelope volume envelope_volume501300 ų
Hydration-shell volume shell_volume86955 ų
Envelope diameter envelope_diameter152.5 Å
Shell Rg shell_rg53.72 Å
Envelope Rg envelope_rg45.58 Å
Shape Rg shape_rg47.24 Å
Total Rg total_rg47.49 Å
Total atoms total_atoms19669
Residues n_residues2033
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 dmax153.5 Å
Rg (real space) rg_real47.69 Å
Rg uncertainty (real space) rg_real_error1.04 Å
I(0) (real space) i0_real1.7220e+09
I(0) uncertainty (real space) i0_real_error3.0510e+07
Rg (reciprocal space) rg_reciprocal48.01 Å
I(0) (reciprocal space) i0_reciprocal1722000000.0000
Solution quality estimate total_estimate0.8178
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary65.1 Å
Skewness Skewness skewness0.091
Kurtosis Kurtosis kurtosis-0.501
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha126400000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

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8. Citations (1)

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9. Files and Curves (10)