Histone H4
Xenopus laevis
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 × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts | Chain B； UniProt 16–103 Chain F； UniProt 16–103 | Not recorded | DNA Tracking Strand × 1 DNA Lagging Strand × 1 Histone H2A × 2 （Q6AZJ8） Histone H2B 1.1 × 2 （P02281） Chromo domain-containing protein 1 × 1 （P32657） Histone H3 × 2 （A0A310TTQ1） | ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE | Resolution 2.54 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 9N6H | 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 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 oligomeric state 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 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | 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 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
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 construct 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 construct 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 construct 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Mutation：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 construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain B
1–103（103 aa）
Chain 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 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 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 construct 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | MN MANGANESE (II) ION × 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 oligomeric state 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | MN MANGANESE (II) ION × 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 construct 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 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 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 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 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 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 construct 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 construct 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric |
Chain 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 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 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 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 construct 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 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 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 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 oligomeric state 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 oligomeric state 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 construct 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 construct 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 construct 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric |
Chain 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 construct 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | 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 construct 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | 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 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 construct 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain B
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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | 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 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE-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 oligomeric state 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 oligomeric state 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain B
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 |
| 6W5I Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class01) Deposited 2020-03-13 | Different construct Different oligomeric state Different 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 6.90 Å |
| 6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 | Different construct Different oligomeric state Different 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 construct Different oligomeric state 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 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 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 oligomeric state 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；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 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 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 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 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 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 Different structure-quality metrics | 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 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.38 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 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 construct 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；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 construct Different oligomeric state 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 construct Different oligomeric state 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 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 construct 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 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 construct 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 construct Different oligomeric state Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
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 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 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 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 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 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.90 Å |
| 7XFH Structure of nucleosome-AAG complex (A-30I, post-catalytic state) Deposited 2022-04-01 | Different construct 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.90 Å |
| 7XFJ Structure of nucleosome-AAG complex (T-50I, post-catalytic state) Deposited 2022-04-01 | Different construct 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.80 Å |
| 7XFM Structure of nucleosome-AAG complex (A-53I, post-catalytic state) Deposited 2022-04-01 | Different construct 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen 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 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 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 construct 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 construct 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 construct 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 construct 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 construct 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 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 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 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 construct 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 construct 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 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 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 construct 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 construct 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 construct 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 construct 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 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 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 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 construct 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 construct 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 construct 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 construct 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 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 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 construct 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 construct 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 construct 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 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 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 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 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 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 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 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 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8VX6 Human OGG1 bound at the nucleosomal DNA entry site Deposited 2024-02-03 | Different construct 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 construct 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 construct 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；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 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 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 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 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 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 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 4.18 Å |
| 9CB7 DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, Ino80-Nucleosome Deposited 2024-06-18 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
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 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 construct Different oligomeric state 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 construct 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 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 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 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9EGZ RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 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
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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9EIL SIRT6 bound to an H3K27Ac nucleosome Deposited 2024-11-26 | Different construct 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 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 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 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；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 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 | 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 construct 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 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 construct 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 construct 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain 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 |
| 9N6I 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex Deposited 2025-02-05 | 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 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 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 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 construct 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain 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 oligomeric state 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；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 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；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 oligomeric state 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 oligomeric state 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 oligomeric state 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 construct 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 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 oligomeric state 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 construct 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 construct 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 construct 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY 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 oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY 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 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 construct 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY 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 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 construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY 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 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 oligomeric state Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
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 oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 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 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 construct 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 | 3 |
| Chains and sequence ranges | Author chain B； PDBConstruct 1–88； UniProt 16–103 Author chain F； PDBConstruct 1–88； UniProt 16–103 |
