Current Protein Identity：P02281
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1AOI COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) AND 146 BP LONG DNA FRAGMENT Deposited 1997-07-03 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
27–125（99 aa）
Fragment：HISTONE H2B
Chain H
27–125（99 aa）
Fragment：HISTONE H2B
|
Mutation：A7P Mutation：A7P | MN MANGANESE (II) ION × 6 | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 2.80 Å R-free 0.302 |
| 1F66 2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z Deposited 2000-06-20 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | MN MANGANESE (II) ION × 15 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.60 Å R-free 0.249 |
| 1KX3 X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution Deposited 2002-01-31 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | MN MANGANESE (II) ION × 13 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.275 |
| 1KX4 X-Ray Structure of the Nucleosome Core Particle, NCP146b, at 2.6 A Resolution Deposited 2002-01-31 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.60 Å R-free 0.300 |
| 1KX5 X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution Deposited 2002-01-31 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | MN MANGANESE (II) ION × 14 CL CHLORIDE ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 1.94 Å R-free 0.275 |
| 1M18 LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA Deposited 2002-06-18 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | MN MANGANESE (II) ION × 11 1SZ N-[5-[[4-[[5-[[5-[[5-[[5-[[3-[3-(dimethylamino)propylamino]-3-oxidanylidene-propyl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]amino]-4-oxidanylidene-butyl]carbamoyl]-1-methyl-pyrrol-3-yl]-1-methyl-4-[[1-methyl-4-[(1-methylimidazol-2-yl)carbonylamino]pyrrol-2-yl]carbonylamino]imidazole-2-carboxamide × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；Manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.45 Å R-free 0.257 |
| 1P34 Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.70 Å R-free 0.270 |
| 1P3A Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 3.00 Å R-free 0.260 |
| 1P3B Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 3.00 Å R-free 0.286 |
| 1P3F Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.90 Å R-free 0.272 |
| 1P3G Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.70 Å R-free 0.265 |
| 1P3I Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.30 Å R-free 0.275 |
| 1P3K Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.90 Å R-free 0.291 |
| 1P3L Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.40 Å R-free 0.265 |
| 1P3M Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.90 Å R-free 0.270 |
| 1P3O Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.75 Å R-free 0.276 |
| 1P3P Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants Deposited 2003-04-17 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；MnCl2, KCl, Potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.70 Å R-free 0.268 |
| 1ZBB Structure of the 4_601_167 Tetranucleosome Deposited 2005-04-08 | Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 36-meric（36） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
Chain d
1–125（125 aa）
Chain h
1–125（125 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.75；294 K；magnesium chloride, potassium chloride, potassium cacodylate, trisCl, pH 6.75, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 9.00 Å |
| 2F8N 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes Deposited 2005-12-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain H
4–125（122 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；34 to 37.5mM KCl and 40-45mM MnCl2, 5mM Potassium Cacodylate, Sample concentration: 8-12 mg/ml, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.90 Å R-free 0.269 |
| 2FJ7 Crystal structure of Nucleosome Core Particle Containing a Poly (dA.dT) Sequence Element Deposited 2005-12-31 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；20 to 35 mM KCl, 34 to 48 mM MnCl2, and 5mM K-cacodylate pH 6.0 , VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 3.20 Å R-free 0.350 |
| 2NZD Nucleosome core particle containing 145 bp of DNA Deposited 2006-11-23 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–125（125 aa）
Chain H
1–125（125 aa）
|
Not recorded | MN MANGANESE (II) ION × 11 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.65 Å R-free 0.283 |
| 3B6F Nucleosome core particle treated with cisplatin Deposited 2007-10-29 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K
|
Resolution 3.45 Å R-free 0.402 |
| 3B6G Nucleosome core particle treated with oxaliplatin Deposited 2007-10-29 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K
|
Resolution 3.45 Å R-free 0.435 |
| 3KWQ Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Deposited 2009-12-01 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
34–126（93 aa）
Fragment：UNP residues 34-126
Chain H
34–126（93 aa）
Fragment：UNP residues 34-126
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 3.50 Å R-free 0.315 |
| 3KXB Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Deposited 2009-12-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S33T Mutation：S33T | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；Crystals were grown by vapor diffusion in 8 20 days at 20 C using a droplet containing 4.0 mg ml−1 core particle 50 mM KCl, 70 75 mM MnCl , and 20 mM potassium cacodylate, pH 6.0, surrounded by silicon oil DC200 (110mPa s; Fluka) and equilibrated against 40 46 mM MnCl2, 35 40 mM KCl and 20 mM potassium cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 293K
|
Resolution 3.20 Å R-free 0.292 |
| 3LEL Structural Insight into the Sequence-Dependence of Nucleosome Positioning Deposited 2010-01-15 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | MN MANGANESE (II) ION × 15 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85mM MnCl2, 60mM KCl, 20mM K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.95 Å R-free 0.300 |
| 3LEL Structural Insight into the Sequence-Dependence of Nucleosome Positioning Deposited 2010-01-15 | Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain N
2–126（125 aa）
Chain R
2–126（125 aa）
|
Not recorded | MN MANGANESE (II) ION × 19 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85mM MnCl2, 60mM KCl, 20mM K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.95 Å R-free 0.300 |
| 3LJA Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome Deposited 2010-01-26 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 45 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, EVAPORATION
|
Resolution 2.75 Å R-free 0.259 |
| 3LZ0 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 1) Deposited 2010-03-01 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K cacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.50 Å R-free 0.318 |
| 3LZ1 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 2) Deposited 2010-03-01 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；Kcacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.50 Å R-free 0.319 |
| 3MGP Binding of Cobalt ions to the Nucleosome Core Particle Deposited 2010-04-07 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | CL CHLORIDE ION × 4 CO COBALT (II) ION × 43 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 2.44 Å R-free 0.282 |
| 3MGQ Binding of Nickel ions to the Nucleosome Core Particle Deposited 2010-04-07 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | NI NICKEL (II) ION × 47 CL CHLORIDE ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 2.65 Å R-free 0.276 |
| 3MGR Binding of Rubidium ions to the Nucleosome Core Particle Deposited 2010-04-07 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | CL CHLORIDE ION × 4 RB RUBIDIUM ION × 5 MN MANGANESE (II) ION × 14 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 2.30 Å R-free 0.267 |
| 3MGS Binding of Cesium ions to the Nucleosome Core particle Deposited 2010-04-07 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | CL CHLORIDE ION × 4 CS CESIUM ION × 12 MN MANGANESE (II) ION × 14 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 3.15 Å R-free 0.238 |
| 3MNN A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core Deposited 2010-04-22 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RU RUTHENIUM ION × 3 MML 1-methyl-4-(1-methylethyl)benzene × 3 PTW 1,3,5-triaza-7-phosphatricyclo[3.3.1.1~3,7~]decane × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；55mM KCl, 85mM MnCl2, 20mM K-Cacodylate, pH 6, VAPOR DIFFUSION, temperature 291K
|
Resolution 2.50 Å R-free 0.277 |
| 3MVD Crystal structure of the chromatin factor RCC1 in complex with the nucleosome core particle Deposited 2010-05-04 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；294 K；25 mM sodium acetate buffer, 25 mM sodium citrate, 1 mM DTT, 6 % PEG2000-MME, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 2.90 Å R-free 0.215 |
| 3O62 Nucleosome core particle modified with a cisplatin 1,3-cis-{Pt(NH3)2}2+-d(GpTpG) intrastrand cross-link Deposited 2010-07-28 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | CPT Cisplatin × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；40-46 mM MnCl2, 30-45 mM KCl, and 20 mM potassium cacodylate pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 3.22 Å R-free 0.306 |
| 3REH 2.5 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Deposited 2011-04-04 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 15 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；KCl, MnCl2, K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.50 Å R-free 0.270 |
| 3REI 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride Deposited 2011-04-04 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | PT PLATINUM (II) ION × 49 SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 2 | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 2.65 Å R-free 0.276 |
| 3REJ 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Deposited 2011-04-04 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | MN MANGANESE (II) ION × 13 SO4 SULFATE ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.55 Å R-free 0.262 |
| 3REK 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Oxaliplatin Deposited 2011-04-04 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 PT PLATINUM (II) ION × 40 SO4 SULFATE ION × 3 | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 2.60 Å R-free 0.281 |
| 3REL 2.7 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Triamminechloroplatinum(II) Chloride Deposited 2011-04-04 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 PT PLATINUM (II) ION × 48 SO4 SULFATE ION × 3 | X-RAY DIFFRACTION | mmCIF provides none of the parsed conditions | Resolution 2.70 Å R-free 0.302 |
| 3TU4 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Deposited 2011-09-15 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
Resolution 3.00 Å R-free 0.241 |
| 3TU4 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Deposited 2011-09-15 | Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
Resolution 3.00 Å R-free 0.241 |
| 3UT9 Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601' Derivative (NCP-601L) Deposited 2011-11-25 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 29 K POTASSIUM ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.20 Å R-free 0.289 |
| 3UTA Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence Containing Two TTAAA elements (NCP-TA2) Deposited 2011-11-25 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 17 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.07 Å R-free 0.266 |
| 3UTB Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite Sequence (NCP146b) Deposited 2011-11-25 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | MN MANGANESE (II) ION × 21 SO4 SULFATE ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.20 Å R-free 0.275 |
| 4J8U X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)osmium(II) Deposited 2013-02-15 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | SO4 SULFATE ION × 3 ELJ chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)osmium(II) × 3 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.38 Å R-free 0.280 |
| 4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 | Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric（5） Consistent with all polymers |
Chain D
2–126（125 aa）
|
Not recorded | SO4 SULFATE ION × 1 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.58 Å R-free 0.273 |
| 4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 | Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric（5） Consistent with all polymers |
Chain H
2–126（125 aa）
|
Not recorded | SO4 SULFATE ION × 2 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.58 Å R-free 0.273 |
| 4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 | Assembly 3 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | SO4 SULFATE ION × 3 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 2 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.58 Å R-free 0.273 |
| 4J8W X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) Deposited 2013-02-15 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | SO4 SULFATE ION × 3 1MK chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) × 3 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.41 Å R-free 0.275 |
| 4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 | Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric（5） Consistent with all polymers |
Chain D
2–126（125 aa）
|
Not recorded | SO4 SULFATE ION × 1 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.87 Å R-free 0.280 |
| 4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 | Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric（5） Consistent with all polymers |
Chain H
2–126（125 aa）
|
Not recorded | SO4 SULFATE ION × 2 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.87 Å R-free 0.280 |
| 4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 | Assembly 3 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | SO4 SULFATE ION × 3 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 2 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.87 Å R-free 0.280 |
| 4KGC Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM Deposited 2013-04-29 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | HRU (ethane-1,2-diamine-kappa~2~N,N')[(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)cyclohexane-1,2,3,4,5,6-hexayl]ruthenium × 4 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.69 Å R-free 0.282 |
| 4KHA Structural basis of histone H2A-H2B recognition by the essential chaperone FACT Deposited 2013-04-30 | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
34–126（93 aa）
Fragment：UNP residues 652-945 and 34-126
|
Not recorded | CL CHLORIDE ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；manual setup 1ul protein (15 mg / ml) plus 1 ul crystallization buffer (7.25% [vol/vol] PEG8000, 0.2 M MgCl2, 0.1 M Tris pH 7.8), VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.35 Å R-free 0.229 |
| 4LD9 Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle Deposited 2013-06-24 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；293.15 K；50 mM MES pH 6.5, 12% PEG 400, 12 mM MnCl2, 100 mM NaCl, 10 mM EDTA, VAPOR DIFFUSION, temperature 293.15K
|
Resolution 3.31 Å R-free 0.295 |
| 4R8P Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle Deposited 2014-09-02 | Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
Modified micro batch under oil；pH 7.5；294 K；25 mM HEPES pH 7.5, 80 mM NH4NO3, 3 % PEG2000-MME, Modified micro batch under oil, temperature 294K
|
Resolution 3.28 Å R-free 0.245 |
| 4WU8 Structure of trPtNAP-NCP145 Deposited 2014-10-31 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Mutation：S29T Mutation：S29T | CX3 [2-(3-{bis[2-(amino-kappaN)ethyl]amino-kappaN}propyl)-1H-benzo[de]isoquinoline-1,3(2H)-dionato(2-)]platinum(1+) × 2 SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Manganese chloride, potassium chloride, potassium cacodylate
|
Resolution 2.45 Å R-free 0.263 |
| 4WU9 Structure of cisPtNAP-NCP145 Deposited 2014-10-31 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Mutation：S29T Mutation：S29T | SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 CX8 [2-{3-[(2-{[2-(amino-kappaN)ethyl]amino-kappaN}ethyl)amino-kappaN]propyl}-1H-benzo[de]isoquinoline-1,3(2H)-dionato(3-)]platinum × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Manganese chloride, potassium chloride, potassium cacodylate
|
Resolution 2.60 Å R-free 0.273 |
| 4XUJ Nucleosome core particle containing adducts from treatment with a thiomorpholine-substituted [(eta-6-p-cymene)Ru(3-hydroxy-2-pyridone)Cl] compound Deposited 2015-01-26 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Fragment：UNP residues 2-126
Chain H
2–126（125 aa）
Fragment：UNP residues 2-126
|
Not recorded | SO4 SULFATE ION × 3 4A6 [(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)benzene]ruthenium × 3 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40mM MnCl2, 30mM KCl, 20mM K-Cacodylate
|
Resolution 3.18 Å R-free 0.299 |
| 4XZQ Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-02-04 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
34–126（93 aa）
Fragment：residues 34-126
Chain H
34–126（93 aa）
Fragment：residues 34-126
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292.15 K；potassium chloride, potassium cacodylate, manganese chloride
|
Resolution 2.40 Å R-free 0.299 |
| 4YS3 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-03-16 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
34–126（93 aa）
Fragment：residues 34-126
Chain H
34–126（93 aa）
Fragment：residues 34-126
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.9；292.15 K；postassium chloride, manganese chloride, cacodylate
|
Resolution 3.00 Å R-free 0.279 |
| 4Z66 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-04-03 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
33–126（94 aa）
Chain H
33–126（94 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292.15 K；potassium chloride, potassium cacodylate, manganese chloride
|
Resolution 2.50 Å R-free 0.296 |
| 4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 16 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
|
Resolution 3.82 Å R-free 0.256 |
| 4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 | Assembly 2 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain N
5–126（122 aa）
Chain R
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 16 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
|
Resolution 3.82 Å R-free 0.256 |
| 5CP6 Nucleosome Core Particle with Adducts from the Anticancer Compound, [(eta6-5,8,9,10-tetrahydroanthracene)Ru(ethylenediamine)Cl][PF6] Deposited 2015-07-21 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | RUH (ethane6-5,8,9,10-tetrahydroanthracene)Ru(II)(ethylene-diamine)Cl × 3 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.60 Å R-free 0.251 |
| 5DNM Nucleosome core particle containing adducts of ruthenium(II)-toluene PTA complex Deposited 2015-09-10 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RAX dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate
|
Resolution 2.81 Å R-free 0.241 |
| 5DNN Nucleosome core particle containing adducts of gold(I)-triethylphosphane and ruthenium(II)-toluene PTA complexes Deposited 2015-09-10 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | AUF triethylphosphanuidylgold(1+) × 2 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RAX dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate
|
Resolution 2.80 Å R-free 0.236 |
| 5E5A Crystal structure of the chromatin-tethering domain of Human cytomegalovirus IE1 protein bound to the nucleosome core particle Deposited 2015-10-08 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | MG MAGNESIUM ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.2；289 K；sodium cacodylate, magnesium
acetate, 2-methyl-2,4-pentanediol
|
Resolution 2.81 Å R-free 0.242 |
| 5F99 X-ray Structure of the MMTV-A Nucleosome Core Particle Deposited 2015-12-09 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | CL CHLORIDE ION × 4 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；sample was mixed 1:1 with 10 mM K-cacodylate, pH 6.0, 180 mM MgCl2, 50 mM KCl and equilibrated against a 1:4 dilution of the same solution
|
Resolution 2.63 Å R-free 0.252 |
| 5G2E Structure of the Nap1 H2A H2B complex Deposited 2016-04-07 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain L
28–126（99 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
10-15% W/V PEG3350; 200 MM LICL
|
Resolution 6.70 Å R-free 0.310 |
| 5G2E Structure of the Nap1 H2A H2B complex Deposited 2016-04-07 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain H
28–126（99 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
10-15% W/V PEG3350; 200 MM LICL
|
Resolution 6.70 Å R-free 0.310 |
| 5G2E Structure of the Nap1 H2A H2B complex Deposited 2016-04-07 | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain D
28–126（99 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
10-15% W/V PEG3350; 200 MM LICL
|
Resolution 6.70 Å R-free 0.310 |
| 5G2E Structure of the Nap1 H2A H2B complex Deposited 2016-04-07 | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain T
28–126（99 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
10-15% W/V PEG3350; 200 MM LICL
|
Resolution 6.70 Å R-free 0.310 |
| 5G2E Structure of the Nap1 H2A H2B complex Deposited 2016-04-07 | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain X
28–126（99 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
10-15% W/V PEG3350; 200 MM LICL
|
Resolution 6.70 Å R-free 0.310 |
| 5G2E Structure of the Nap1 H2A H2B complex Deposited 2016-04-07 | Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain P
28–126（99 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
10-15% W/V PEG3350; 200 MM LICL
|
Resolution 6.70 Å R-free 0.310 |
| 5HQ2 Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle Deposited 2016-01-21 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: hexadecameric（16） Consistent with all polymers |
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
MICROBATCH；pH 5.5；277 K；25 mM sodium acetate pH 5.5, 40 mM sodium citrate,1 mM DTT, 6% PEG2000-MME
|
Resolution 4.50 Å R-free 0.397 |
| 5NL0 Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1 Deposited 2017-04-03 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；293.15 K；Mix of equal volumes of the nucleosome/H1 complex (25-30 microM) and a crystallization solution composed of MPD (6% v/v), 50 mM NaCl, and 50 mM sodium potassium phosphate pH 6.4.
|
Resolution 5.40 Å R-free 0.265 |
| 5NL0 Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1 Deposited 2017-04-03 | Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers |
Chain N
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；293.15 K；Mix of equal volumes of the nucleosome/H1 complex (25-30 microM) and a crystallization solution composed of MPD (6% v/v), 50 mM NaCl, and 50 mM sodium potassium phosphate pH 6.4.
|
Resolution 5.40 Å R-free 0.265 |
| 5O9G Structure of nucleosome-Chd1 complex Deposited 2017-06-19 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–125（121 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 5OMX X-ray Structure of the H2A-N38C Nucleosome Core Particle Deposited 2017-08-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | MN MANGANESE (II) ION × 33 CL CHLORIDE ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；8 mg/ml sample was mixed 1:1 with 10 mM K-Cacodylate (pH 6.0), 140-150 mM MnCl2, 100 KCl. and equilibrated against a 1:4 dilution of the same solution
|
Resolution 2.32 Å R-free 0.259 |
| 5ONG X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer Deposited 2017-08-03 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | MN MANGANESE (II) ION × 20 CL CHLORIDE ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；Sample was mixed in a 1:1 ratio with 10 mM Na-cacodylate, pH 6.0, 130-180 mM MnCl2, 100-160 mM KCl and equilibrated against a 1:4 dilution of the same solution
|
Resolution 2.80 Å R-free 0.247 |
| 5ONW X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two H2A/H2B dimers crosslinked via H2A N38C Deposited 2017-08-04 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | MN MANGANESE (II) ION × 20 CL CHLORIDE ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；Sample was mixed in a 1:1 ratio with 10 mM Na-cacodylate, pH 6.0, 160-210 mM MnCl2, 140-200 mM KCl and equilibrated against a 1:4 dilution of the same solution
|
Resolution 2.80 Å R-free 0.254 |
| 5OXV Structure of the 4_601_157 tetranucleosome (C2 form) Deposited 2017-09-07 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric（18） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
Chain N
1–126（126 aa）
Chain R
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；30-60 mM KCl, 90-110 mM MgCl2 and 5 mM Na-cacodylate, pH 6
|
Resolution 6.72 Å R-free 0.352 |
| 5OY7 Structure of the 4_601_157 tetranucleosome (P1 form) Deposited 2017-09-07 | Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
Chain L
1–126（126 aa）
Chain P
1–126（126 aa）
Chain T
1–126（126 aa）
Chain X
1–126（126 aa）
Chain b
1–126（126 aa）
Chain f
1–126（126 aa）
|
Not recorded | CL CHLORIDE ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；30-60 mM KCl, 90-110 mM MgCl2 and 5 mM Na-cacodyalte, pH 6.0
|
Resolution 5.77 Å R-free 0.238 |
| 5X0X Complex of Snf2-Nucleosome complex with Snf2 bound to position +6 of the nucleosome Deposited 2017-01-23 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.97 Å |
| 5X0Y Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome Deposited 2017-01-23 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.69 Å |
| 5XF6 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker Deposited 2017-04-07 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 EDN ETHANE-1,2-DIAMINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0
|
Resolution 2.63 Å R-free 0.254 |
| 5Z3L Structure of Snf2-nucleosome complex in apo state Deposited 2018-01-08 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.31 Å |
| 5Z3O Structure of Snf2-nucleosome complex in ADP state Deposited 2018-01-08 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.62 Å |
| 5Z3U Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state Deposited 2018-01-08 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.31 Å |
| 5Z3V Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state Deposited 2018-01-08 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.22 Å |
| 6ESF Nucleosome : Class 1 Deposited 2017-10-20 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 6ESG Nucleosome breathing : Class 2 Deposited 2017-10-20 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.40 Å |
| 6ESH Nucleosome breathing : Class 3 Deposited 2017-10-20 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.10 Å |
| 6ESI Nucleosome breathing : Class 4 Deposited 2017-10-20 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.30 Å |
| 6I84 Structure of transcribing RNA polymerase II-nucleosome complex Deposited 2018-11-19 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain R
5–126（122 aa）
Chain W
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 6IRO the crosslinked complex of ISWI-nucleosome in the ADP-bound state Deposited 2018-11-13 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 6J99 Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome Deposited 2019-01-22 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T, K117C Mutation：S29T, K117C | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 6JM9 cryo-EM structure of DOT1L bound to unmodified nucleosome Deposited 2019-03-07 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
34–126（93 aa）
Chain H
34–126（93 aa）
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.30 Å |
| 6JMA cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome Deposited 2019-03-07 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
34–126（93 aa）
Chain H
34–126（93 aa）
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.80 Å |
| 6JYL The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state Deposited 2019-04-26 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot 1.5s
|
Resolution 3.37 Å |
| 6K01 Crystal structure of xH2A-H2B Deposited 2019-05-05 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
28–126（99 aa）
|
Mutation：S30T | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Ammonium sulfate, 0.1M HEPES pH=7.5, 25% PEG 3350
|
Resolution 2.84 Å R-free 0.278 |
| 6K1P The complex of ISWI-nucleosome in the ADP.BeF-bound state Deposited 2019-05-10 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8.5；10 mM Tris, 50 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 1.5s
|
Resolution 3.87 Å |
| 6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T/K117T Mutation：S29T/K117T | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T/K117C Mutation：S29T/K117C | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 6KIW Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T/K117C Mutation：S29T/K117C | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 6KIX Cryo-EM structure of human MLL1-NCP complex, binding mode1 Deposited 2019-07-20 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T/K117C Mutation：S29T/K117C | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 6KIZ Cryo-EM structure of human MLL1-NCP complex, binding mode2 Deposited 2019-07-20 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T/K117C Mutation：S29T/K117C | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 6N1Z Importin-9 bound to H2A-H2B Deposited 2018-11-12 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
5–126（122 aa）
Fragment：HISTONE H2B 1.1
|
Mutation：S33T | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.04 M MES, 0.11 M potassium acetate, 2 mM magnesium acetate, 2 mM DTT, 3.0 M potassium formate, 25% glycerol
|
Resolution 2.70 Å R-free 0.238 |
| 6N1Z Importin-9 bound to H2A-H2B Deposited 2018-11-12 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain F
5–126（122 aa）
Fragment：HISTONE H2B 1.1
|
Mutation：S33T | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.04 M MES, 0.11 M potassium acetate, 2 mM magnesium acetate, 2 mM DTT, 3.0 M potassium formate, 25% glycerol
|
Resolution 2.70 Å R-free 0.238 |
| 6NJ9 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex Deposited 2019-01-02 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S32T, K120C Mutation：S32T, K120C | SAM S-ADENOSYLMETHIONINE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions
Cryogen ETHANE；Blot once for 3.5 seconds before freezing.
|
Resolution 2.96 Å |
| 6NN6 Structure of Dot1L-H2BK120ub nucleosome complex Deposited 2019-01-14 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S33T, K121C Mutation：S33T, K121C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 6NOG Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome Deposited 2019-01-16 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S32T, K120C Mutation：S32T, K120C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions
Cryogen ETHANE；Blot once for 3.5 seconds before freezing
|
Resolution 3.90 Å |
| 6NQA Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex Deposited 2019-01-19 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S32T, K120C Mutation：S32T, K120C | SAM S-ADENOSYLMETHIONINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions
Cryogen ETHANE；Blot once for 3.5 seconds before freezing.
|
Resolution 3.54 Å |
| 6NZO Set2 bound to nucleosome Deposited 2019-02-14 | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | ZN ZINC ION × 3 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 6O96 Dot1L bound to the H2BK120 Ubiquitinated nucleosome Deposited 2019-03-13 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：K120C, S32T Mutation：K120C, S32T | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen PROPANE；blotted for 3s before plunging
|
Resolution 3.50 Å |
| 6OM3 Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle Deposited 2019-04-18 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Mutation：S32T Mutation：S32T | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；277.15 K；6 mM Na-Cacodylate pH 6.0, 0.4 mM Spermine-HCl, 2 mM MgCl2 and 1.75% v/v PEG 400
|
Resolution 3.30 Å R-free 0.250 |
| 6OM3 Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle Deposited 2019-04-18 | Assembly 2 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain P
1–126（126 aa）
Chain T
1–126（126 aa）
|
Mutation：S32T Mutation：S32T | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；277.15 K；6 mM Na-Cacodylate pH 6.0, 0.4 mM Spermine-HCl, 2 mM MgCl2 and 1.75% v/v PEG 400
|
Resolution 3.30 Å R-free 0.250 |
| 6PA7 The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. Deposited 2019-06-11 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | CL CHLORIDE ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers |
Chain J
5–126（122 aa）
Chain N
5–126（122 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.20 Å |
| 6PWW Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome Deposited 2019-07-23 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain J
5–126（122 aa）
Chain N
5–126（122 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 6PWX Cryo-EM structure of RbBP5 bound to the nucleosome Deposited 2019-07-23 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain J
5–126（122 aa）
Chain N
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 6PX1 Set2 bound to nucleosome Deposited 2019-07-24 | Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 6PX3 Set2 bound to nucleosome Deposited 2019-07-24 | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | ZN ZINC ION × 3 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 6R1U Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2 Deposited 2019-03-15 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.36 Å |
| 6RYR Nucleosome-CHD4 complex structure (single CHD4 copy) Deposited 2019-06-11 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 6RYU Nucleosome-CHD4 complex structure (two CHD4 copies) Deposited 2019-06-12 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 6S01 Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome Deposited 2019-06-13 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 4 seconds before plunging
|
Resolution 3.20 Å |
| 6T9L SAGA DUB module bound to a ubiqitinated nucleosome Deposited 2019-10-28 | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers |
Chain D
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 8 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 4 seconds before plunging
|
Resolution 3.60 Å |
| 6TDA Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome Deposited 2019-11-08 | Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 15.00 Å |
| 6TEM CENP-A nucleosome core particle with 145 base pairs of the Widom 601 sequence by cryo-EM Deposited 2019-11-12 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.90 Å |
| 6UGM Structural basis of COMPASS eCM recognition of an unmodified nucleosome Deposited 2019-09-26 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric（18） Consistent with all polymers |
Chain H
2–126（125 aa）
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 6UXW SWI/SNF nucleosome complex with ADP-BeFx Deposited 2019-11-08 | Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric（28） Consistent with all polymers |
Chain U
5–126（122 aa）
Chain Y
5–126（122 aa）
|
Not recorded | PO4 PHOSPHATE ION × 12 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9；10 mM HEPES, pH 7.9, 10 mM MgCl2, 50 mM KCl, 1 mM DTT, 5% glycerol, 0.05% NP-40
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.96 Å |
| 6VEN Yeast COMPASS in complex with a ubiquitinated nucleosome Deposited 2020-01-02 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric（18） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：K120C, S30T Mutation：K120C, S30T | ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot force 5
3.5 sec blot time
|
Resolution 3.37 Å |
| 6VYP Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate Deposited 2020-02-27 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S32T Mutation：S32T | FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
MICROBATCH；pH 7.5；277 K；25 mM HEPES pH7.5,
75 mM triammonium citrate,
10% PEG2000-MME,
Modified Microbatch under oil
|
Resolution 4.99 Å R-free 0.277 |
| 6VYP Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate Deposited 2020-02-27 | Assembly 2 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain d
5–126（122 aa）
Chain h
5–126（122 aa）
|
Mutation：S32T Mutation：S32T | FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
MICROBATCH；pH 7.5；277 K；25 mM HEPES pH7.5,
75 mM triammonium citrate,
10% PEG2000-MME,
Modified Microbatch under oil
|
Resolution 4.99 Å R-free 0.277 |
| 6W4L The crystal structure of a single chain H2B-H2A histone chimera from Xenopus laevis Deposited 2020-03-11 | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
34–126（93 aa）
|
Not recorded | PPV PYROPHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.9；291 K；0.2M sodium thiocyanate, 20% PEG3350
|
Resolution 1.31 Å R-free 0.206 |
| 6W5I Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class01) Deposited 2020-03-13 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain J
5–126（122 aa）
Chain N
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.90 Å |
| 6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain J
5–126（122 aa）
Chain N
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 6W5N Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Deposited 2020-03-13 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain J
5–126（122 aa）
Chain N
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.00 Å |
| 6WKR PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome Deposited 2020-04-16 | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: octadecameric（18） Consistent with all polymers |
Chain M
1–126（126 aa）
Chain S
1–126（126 aa）
|
Not recorded | MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 6WZ5 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-13 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.20 Å |
| 6WZ9 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-13 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 6X0N Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-16 | Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
Chain d
5–126（122 aa）
Chain h
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 10.00 Å |
| 6ZHX Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: nucleosome class. Deposited 2020-06-24 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Blot time 2.5 s, blot force 0.
Two sample applications and blots were performed before vitrification.
|
Resolution 2.50 Å |
| 6ZHY Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: hexasome class. Deposited 2020-06-24 | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric（9） Consistent with all polymers |
Chain D
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Blot time 2.5 s, blot force 0.
Two sample applications and blots were performed before vitrification.
|
Resolution 3.00 Å |
| 7AT8 Histone H3 recognition by nucleosome-bound PRC2 subunit EZH2. Deposited 2020-10-29 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain G
5–126（122 aa）
Chain K
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 7 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 4.40 Å |
| 7E8I Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin Deposited 2021-03-01 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7EG6 Snf5 Finger Helix bound to the nucleosome Deposited 2021-03-24 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7EGP The structure of SWI/SNF-nucleosome complex Deposited 2021-03-24 | Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric（21） Consistent with all polymers |
Chain R
5–126（122 aa）
Chain V
5–126（122 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.90 Å |
| 7ENN The structure of ALC1 bound to the nucleosome Deposited 2021-04-18 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7K6P Active state Dot1 bound to the unacetylated H4 nucleosome Deposited 2020-09-21 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
33–125（93 aa）
Chain H
33–125（93 aa）
|
Mutation：K120C,S32T Mutation：K120C,S32T | SAM S-ADENOSYLMETHIONINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7K6Q Active state Dot1 bound to the H4K16ac nucleosome Deposited 2020-09-21 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
33–125（93 aa）
Chain H
33–125（93 aa）
|
Mutation：K120C, S32T Mutation：K120C, S32T | SAM S-ADENOSYLMETHIONINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7KBD Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction) Deposited 2020-10-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.38 Å |
| 7KBE Nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction) Deposited 2020-10-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7KBF H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction) Deposited 2020-10-02 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.42 Å |
| 7M1X Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z Deposited 2021-03-15 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 4.5 seconds before plunging
|
Resolution 3.70 Å |
| 7MBM Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Deposited 2021-04-01 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain J
5–126（122 aa）
Chain N
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.76 Å |
| 7MBN Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Deposited 2021-04-01 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain J
5–126（122 aa）
Chain N
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.02 Å |
| 7NKX RNA polymerase II-Spt4/5-nucleosome-Chd1 structure Deposited 2021-02-19 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain d
5–126（122 aa）
Chain h
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7NKY RNA Polymerase II-Spt4/5-nucleosome-FACT structure Deposited 2021-02-19 | Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 27-meric（27） Consistent with all polymers |
Chain d
5–126（122 aa）
Chain h
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7OH9 Nucleosome with TBP and TFIIA bound at SHL -6 Deposited 2021-05-09 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7OHA nucleosome with TBP and TFIIA bound at SHL +2 Deposited 2021-05-09 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7OHB TBP-nucleosome complex Deposited 2021-05-10 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7OHC Cryo-EM structure of nucleosome core particle composed of the Widom 601 DNA sequence Deposited 2021-05-10 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 7OTQ Cryo-EM structure of ALC1/CHD1L bound to a PARylated nucleosome Deposited 2021-06-10 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；3 uL were applied on grid and immediately blotted for 2.5 s at blot force 0.
|
Resolution 4.80 Å |
| 7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric（17） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S32T, K120C Mutation：S32T, K120C | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.25 Å |
| 7UNC Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome Deposited 2022-04-10 | Assembly 1 Other combination Heteromer；Protein × 29 PDB declaration: 32-meric（32） Consistent with all polymers |
Chain d
5–126（122 aa）
Chain h
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7UND Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) Deposited 2022-04-10 | Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric（33） Consistent with all polymers |
Chain d
5–126（122 aa）
Chain h
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7VDT The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex Deposited 2021-09-07 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7VDV The overall structure of human chromatin remodeling PBAF-nucleosome complex Deposited 2021-09-07 | Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric（24） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7VVU NuA4 HAT module bound to the nucleosome Deposited 2021-11-09 | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain U
1–126（126 aa）
|
Not recorded | CMC CARBOXYMETHYL COENZYME *A × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 3.40 Å |
| 7VVZ NuA4 bound to the nucleosome Deposited 2021-11-09 | Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric（21） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain U
1–126（126 aa）
|
Not recorded | CMC CARBOXYMETHYL COENZYME *A × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 8.80 Å |
| 7X3T Cryo-EM structure of ISW1a-dinucleosome Deposited 2022-03-01 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric（20） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
Chain N
1–126（126 aa）
Chain R
1–126（126 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.40 Å |
| 7X3V Cryo-EM structure of IOC3-N2 nucleosome Deposited 2022-03-01 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.09 Å |
| 7X3W Cryo-EM structure of ISW1-N1 nucleosome Deposited 2022-03-01 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7X3X Cryo-EM structure of N1 nucleosome-RA Deposited 2022-03-01 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7XFC Structure of nucleosome-DI complex (-30I, Apo state) Deposited 2022-04-01 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.90 Å |
| 7XFH Structure of nucleosome-AAG complex (A-30I, post-catalytic state) Deposited 2022-04-01 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.90 Å |
| 7XFI Structure of nucleosome-DI complex (-50I, Apo state) Deposited 2022-04-01 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.90 Å |
| 7XFJ Structure of nucleosome-AAG complex (T-50I, post-catalytic state) Deposited 2022-04-01 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 3.00 Å |
| 7XFL Structure of nucleosome-AAG complex (A-53I, free state) Deposited 2022-04-01 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.80 Å |
| 7XFM Structure of nucleosome-AAG complex (A-53I, post-catalytic state) Deposited 2022-04-01 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 3.10 Å |
| 7XFN Structure of nucleosome-DI complex (-55I, Apo state) Deposited 2022-04-01 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.80 Å |
| 7XNP Structure of nucleosome-AAG complex (A-55I, post-catalytic state) Deposited 2022-04-29 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.90 Å |
| 7XPX Cryo-EM structure of the histone methyltransferase SET8 bound to H4K20Ecx-nucleosome Deposited 2022-05-06 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7YI1 Cryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome Deposited 2022-07-14 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7YI4 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in close state Deposited 2022-07-14 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers |
Chain J
5–126（122 aa）
Chain N
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 5 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.96 Å |
| 7YI5 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in loose state Deposited 2022-07-14 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers |
Chain J
5–126（122 aa）
Chain N
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | ZN ZINC ION × 5 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.96 Å |
| 7YRD histone methyltransferase Deposited 2022-08-09 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
32–126（95 aa）
Chain H
32–126（95 aa）
|
Not recorded | ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7YRG histone methyltransferase Deposited 2022-08-09 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
32–126（95 aa）
Chain H
32–126（95 aa）
|
Mutation：S33T Mutation：S33T | ZN ZINC ION × 2 SAM S-ADENOSYLMETHIONINE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06 | Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric（38） Consistent with all polymers |
Chain d
2–126（125 aa）
Chain h
2–126（125 aa）
|
Not recorded | ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06 | Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric（38） Consistent with all polymers |
Chain d
2–126（125 aa）
Chain h
2–126（125 aa）
|
Not recorded | ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06 | Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric（38） Consistent with all polymers |
Chain d
2–126（125 aa）
Chain h
2–126（125 aa）
|
Not recorded | ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.60 Å |
| 8B0A Cryo-EM structure of ALC1 bound to an asymmetric, site-specifically PARylated nucleosome Deposited 2022-09-07 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 | Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric（42） Consistent with all polymers |
Chain d
1–126（126 aa）
Chain h
1–126（126 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 | Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric（40） Consistent with all polymers |
Chain d
1–126（126 aa）
Chain h
1–126（126 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8BZ1 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Deposited 2022-12-14 | Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric（28） Consistent with all polymers |
Chain d
1–126（126 aa）
Chain h
1–126（126 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8CBN structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Deposited 2023-01-25 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.34 Å |
| 8CBQ structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Deposited 2023-01-25 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8DU4 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Deposited 2022-07-26 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S32T, K120C Mutation：S32T, K120C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.55 Å |
| 8ETT Class1 of the INO80-Hexasome complex Deposited 2022-10-17 | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric（8） Consistent with all polymers |
Chain D
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 6.68 Å |
| 8ETV Class2 of the INO80-Hexasome complex Deposited 2022-10-17 | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric（8） Consistent with all polymers |
Chain D
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 3.16 Å |
| 8EU2 Class3 of the INO80-Hexasome complex Deposited 2022-10-18 | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric（8） Consistent with all polymers |
Chain D
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 2.93 Å |
| 8F86 SIRT6 bound to an H3K9Ac nucleosome Deposited 2022-11-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ZSL [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3aR,5R,6R,6aR)-6-hydroxytetrahydro-2H-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) × 1 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8G6G H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 5 Deposited 2023-02-15 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S33T, K120C Mutation：S33T, K120C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.93 Å |
| 8G6H H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 6 Deposited 2023-02-15 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S33T, K120C Mutation：S33T, K120C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.06 Å |
| 8G6Q H2AK119ub-modified nucleosome ubiquitin position 1 Deposited 2023-02-15 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S33T Mutation：S33T | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.41 Å |
| 8G6S H2AK119ub-modified nucleosome ubiquitin position 2 Deposited 2023-02-15 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S33T Mutation：S33T | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.47 Å |
| 8G86 Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of nucleosome) Deposited 2023-02-17 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 8G88 Human Oct4 bound to nucleosome with human nMatn1 sequence Deposited 2023-02-17 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 8G8B Nucleosome with human nMatn1 sequence in complex with Human Oct4 Deposited 2023-02-17 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 8G8G Interaction of H3 tail in LIN28B nucleosome with Oct4 Deposited 2023-02-17 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8GPN Human menin in complex with H3K79Me2 nucleosome Deposited 2022-08-26 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8KD2 Rpd3S in complex with 187bp nucleosome Deposited 2023-08-09 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers |
Chain R
5–126（122 aa）
Chain V
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.02 Å |
| 8KD3 Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA Deposited 2023-08-09 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers |
Chain R
5–126（122 aa）
Chain V
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8KD4 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1 Deposited 2023-08-09 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers |
Chain R
5–126（122 aa）
Chain V
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.93 Å |
| 8KD5 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2 Deposited 2023-08-09 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric（16） Consistent with all polymers |
Chain R
5–126（122 aa）
Chain V
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8KD6 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3 Deposited 2023-08-09 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers |
Chain R
5–126（122 aa）
Chain V
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.07 Å |
| 8KD7 Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA Deposited 2023-08-09 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers |
Chain R
5–126（122 aa）
Chain V
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.09 Å |
| 8PC5 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex Deposited 2023-06-09 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.02 Å |
| 8PC6 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Deposited 2023-06-09 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 8PEO H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex Deposited 2023-06-14 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.69 Å |
| 8PEP H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Deposited 2023-06-14 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.33 Å |
| 8RUP Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome Deposited 2024-01-31 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric（13） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blotting time, -10 force, no wait time.
|
Resolution 2.42 Å |
| 8RUQ Borealin N-terminus in complex with H3.T3p-nucleosome Deposited 2024-01-31 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blotting time, -10 force, no wait time.
|
Resolution 2.29 Å |
| 8SIY Origin Recognition Complex Associated (ORCA) protein bound to H4K20me3-nucleosome Deposited 2023-04-17 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain F
5–126（122 aa）
Chain J
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8SKZ Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome Deposited 2023-04-20 | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8SVF BAP1/ASXL1 bound to the H2AK119Ub Nucleosome Deposited 2023-05-16 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric（13） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Mutation：S33T Mutation：S33T | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8T3T Structure of Bre1-nucleosome complex - state3 Deposited 2023-06-07 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.21 Å |
| 8T3W Structure of Bre1-nucleosome complex - state2 Deposited 2023-06-07 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 8T3Y Structure of Bre1-nucleosome complex - state1 Deposited 2023-06-08 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20 mM HEPES, pH 7.5, 50 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.47 Å |
| 8T9F Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Deposited 2023-06-23 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 8T9G Automethylated PRC2 dimer bound to nucleosome Deposited 2023-06-23 | Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric（21） Consistent with all polymers |
Chain S
5–126（122 aa）
Chain V
5–126（122 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.20 Å |
| 8T9H Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Deposited 2023-06-24 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.37 Å |
| 8TAS PRC2 monomer bound to nucleosome Deposited 2023-06-27 | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers |
Chain S
5–126（122 aa）
Chain V
5–126（122 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8TB9 PRC2-J119-450 monomer bound to H1-nucleosome Deposited 2023-06-28 | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric（17） Consistent with all polymers |
Chain S
5–126（122 aa）
Chain V
5–126（122 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8THU Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Deposited 2023-07-18 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8TOF Rpd3S bound to an H3K36Cme3 modified nucleosome Deposited 2023-08-03 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric（18） Consistent with all polymers |
Chain d
5–126（122 aa）
Chain h
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | ZN ZINC ION × 5 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8U5H Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome Deposited 2023-09-12 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain M
5–126（122 aa）
Chain S
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.23 Å |
| 8UW1 Cryo-EM structure of DNMT3A1 UDR in complex with H2AK119Ub-nucleosome Deposited 2023-11-05 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.88 Å |
| 8UXQ Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome Deposited 2023-11-09 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain H
2–126（125 aa）
Chain N
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.30 Å |
| 8V25 H2BK120ub-modified nucleosome ubiquitin position 1 Deposited 2023-11-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T, K117C Mutation：S29T, K117C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 8V26 H2BK120ub-modified nucleosome ubiquitin position 2 Deposited 2023-11-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T, K117C Mutation：S29T, K117C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.33 Å |
| 8V27 H2BK120ub-modified nucleosome ubiquitin position 3 Deposited 2023-11-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T, K117C Mutation：S29T, K117C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.34 Å |
| 8V28 H2BK120ub-modified nucleosome ubiquitin position 4 Deposited 2023-11-22 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T, K117C Mutation：S29T, K117C | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.36 Å |
| 8V4Y Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 1) Deposited 2023-11-29 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8V6V Cryo-EM structure of doubly-bound SNF2h-nucleosome complex Deposited 2023-12-03 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8V7L Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 2) Deposited 2023-12-04 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8VO0 H3K36me3-modified nucleosome bound to PRC2_AJ1-450 with histone H3 tail disengaged Deposited 2024-01-14 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain M
40–126（87 aa）
Chain S
38–126（89 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8VOB H3K36me3-modified nucleosome bound to PRC2_AJ1-450 Deposited 2024-01-14 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain M
31–126（96 aa）
Chain S
31–126（96 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8VX5 Nucleosome core particle containing an 8-oxoG damage site Deposited 2024-02-03 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8VX6 Human OGG1 bound at the nucleosomal DNA entry site Deposited 2024-02-03 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S29T Mutation：S29T | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8XAA Structure of NAP1 in complex with H2A-H2B Deposited 2023-12-03 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain J
28–126（99 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris, pH 8.0, 25 % v/v PEG 400
|
Resolution 3.35 Å R-free 0.261 |
| 8XAA Structure of NAP1 in complex with H2A-H2B Deposited 2023-12-03 | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain L
28–126（99 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris, pH 8.0, 25 % v/v PEG 400
|
Resolution 3.35 Å R-free 0.261 |
| 8XJV Structural basis for the linker histone H5-nucleosome binding and chromatin compaction Deposited 2023-12-22 | Assembly 1 Protein–DNA Heteromer；Protein × 108 PDB declaration: 110-meric（110） Consistent with all polymers |
Chain Aa
5–126（122 aa）
Chain Ab
5–126（122 aa）
Chain Ac
5–126（122 aa）
Chain Ad
5–126（122 aa）
Chain Af
5–126（122 aa）
Chain Ag
5–126（122 aa）
Chain At
5–126（122 aa）
Chain J
5–126（122 aa）
Chain M
5–126（122 aa）
Chain N
5–126（122 aa）
Chain O
5–126（122 aa）
Chain P
5–126（122 aa）
Chain Q
5–126（122 aa）
Chain R
5–126（122 aa）
Chain S
5–126（122 aa）
Chain T
5–126（122 aa）
Chain U
5–126（122 aa）
Chain V
5–126（122 aa）
Chain W
5–126（122 aa）
Chain av
5–126（122 aa）
Chain aw
5–126（122 aa）
Chain ax
5–126（122 aa）
Chain ay
5–126（122 aa）
Chain az
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 3.60 Å |
| 8ZVY Alpha-Synuclein with H2a-H2b dimer complex structure. Deposited 2024-06-12 | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
34–126（93 aa）
Chain B
34–126（93 aa）
|
Not recorded | CL CHLORIDE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291.15 K；100 mM Tris pH 8.0 and 10% PEG 8000.
|
Resolution 1.72 Å R-free 0.220 |
| 9B2S Haspin bound to nucleosome in position 1 Deposited 2024-03-16 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S33T Mutation：S33T | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.01 Å |
| 9B2T Haspin bound to nucleosome in position 2 Deposited 2024-03-16 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S33T Mutation：S33T | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.99 Å |
| 9B3P The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome Deposited 2024-03-19 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20mM Tris-HCl, 5mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE；Freezing condition: blot force 0, blot time 4.5 second
|
Resolution 3.00 Å |
| 9C9X S.c INO80 in complex with Xenopus 0/80 nucleosome, Nucleosome Deposited 2024-06-16 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 2.83 Å |
| 9CA7 Cryo-EM structure of human SRCAP-nucleosome complex in the fully-engaged state (composite structure) Deposited 2024-06-17 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric（20） Consistent with all polymers |
Chain R
2–126（125 aa）
Chain T
2–126（125 aa）
|
Not recorded | AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 5 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 9CA8 Cryo-EM structure of human SRCAP-nucleosome complex in the partially-engaged state (composite structure) Deposited 2024-06-17 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric（20） Consistent with all polymers |
Chain R
2–126（125 aa）
Chain T
2–126（125 aa）
|
Not recorded | AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 5 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.92 Å |
| 9CAA Cryo-EM structure of human SRCAP-nucleosome complex in the pre-engaged state (composite structure) Deposited 2024-06-17 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric（20） Consistent with all polymers |
Chain R
2–126（125 aa）
Chain T
2–126（125 aa）
|
Not recorded | AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.04 Å |
| 9CAB Cryo-EM structure of human SRCAP-nucleosome complex in the encounter state (composite structure) Deposited 2024-06-17 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric（20） Consistent with all polymers |
Chain R
2–126（125 aa）
Chain T
2–126（125 aa）
|
Not recorded | AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 5 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.94 Å |
| 9CAN S.c INO80 in complex with Xenopus 0/40 nucleosome Deposited 2024-06-17 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric（20） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 6 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 3.30 Å |
| 9CG9 Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2 Deposited 2024-06-28 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Mutation：S32T Mutation：S32T | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；3 uL of sample was applied to grid.
|
Resolution 2.94 Å |
| 9DBY ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome Deposited 2024-08-24 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Mutation：S33T Mutation：S33T | ZN ZINC ION × 5 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9DDE ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome Deposited 2024-08-28 | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric（15） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Mutation：S33T Mutation：S33T | ZN ZINC ION × 5 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9DG3 ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome Deposited 2024-09-01 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Mutation：S33T Mutation：S33T | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.46 Å |
| 9DGG ncPRC1RYBP bound to unmodified nucleosome Deposited 2024-09-02 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Mutation：S33T Mutation：S33T | ZN ZINC ION × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 9E1L Snf2h bound nucleosome complex - ClassA1 Deposited 2024-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.15 Å |
| 9E1M Snf2h bound nucleosome complex - ClassA2 Deposited 2024-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 9E1N Snf2h bound nucleosome complex-ClassA3 Deposited 2024-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9E1O Snf2h bound nucleosome complex - ClassB1 Deposited 2024-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9E1P Snf2h bound nucleosome complex - ClassB2 Deposited 2024-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 9E1Q Snf2h bound nucleosome complex - ClassB3 Deposited 2024-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9E1R Snf2h bound nucleosome complex - ClassB4 Deposited 2024-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9E1U Snf2h bound nucleosome complex - ClassC1 Deposited 2024-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9E1V Snf2h bound nucleosome complex - ClassC2 Deposited 2024-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9E1W Snf2h bound nucleosome complex - ClassC3 Deposited 2024-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9E1X Snf2h bound nucleosome complex - ClassD1 Deposited 2024-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9E1Y Empty Nucleosome with 601 widom sequence Deposited 2024-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 9EGX RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27 Deposited 2024-11-21 | Assembly 1 Other combination Heteromer；Protein × 29 PDB declaration: 32-meric（32） Consistent with all polymers |
Chain d
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9EGY RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27 Deposited 2024-11-21 | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain d
5–126（122 aa）
Chain h
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9EGZ RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 Deposited 2024-11-21 | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric（35） Consistent with all polymers |
Chain d
5–126（122 aa）
Chain h
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 12 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9EH0 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream Deposited 2024-11-21 | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric（35） Consistent with all polymers |
Chain d
5–126（122 aa）
Chain h
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 9EH1 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream Deposited 2024-11-21 | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric（35） Consistent with all polymers |
Chain d
5–126（122 aa）
Chain h
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9EH2 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream Deposited 2024-11-21 | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric（35） Consistent with all polymers |
Chain h
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9EIL SIRT6 bound to an H3K27Ac nucleosome Deposited 2024-11-26 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ZSL [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3aR,5R,6R,6aR)-6-hydroxytetrahydro-2H-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) × 1 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9F0O The molecular basis and modulation of lamin-specific chromatin interaction Deposited 2024-04-17 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
30–126（97 aa）
Chain H
30–126（97 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 9FH9 Structure of CyclinB1 N-terminus bound to the NCP Deposited 2024-05-27 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 9GD0 Structure of a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric（16） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
Chain N
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9GD1 Structure of Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04 | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric（17） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
Chain N
5–126（122 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 9GD2 Structure of Chd1 bound to a dinucleosome with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04 | Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric（21） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
Chain N
5–126（122 aa）
Chain Q
5–126（122 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 9GD3 Structure of a mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA. Deposited 2024-08-04 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9GEN Recombinant Myeloperoxidase bound to nucleosome core particle Deposited 2024-08-07 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
30–125（96 aa）
Chain H
30–125（96 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.76 Å |
| 9GEO Nucleosome core particle Deposited 2024-08-07 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
30–125（96 aa）
Chain H
30–125（96 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.79 Å |
| 9GEP Native monomeric Myeloperoxidase bound to nucleosome core particle Deposited 2024-08-07 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain D
30–125（96 aa）
Chain H
30–125（96 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.89 Å |
| 9GEQ Native dimeric Myeloperoxidase bound to nucleosome core particle; composite map Deposited 2024-08-07 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Review required |
Chain D
30–125（96 aa）
Chain H
30–125（96 aa）
|
Not recorded | CL CHLORIDE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.12 Å |
| 9GER Native dimeric Myeloperoxidase bound to nucleosome core particle, intermediate state; composite map Deposited 2024-08-07 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Review required |
Chain D
30–125（96 aa）
Chain H
30–125（96 aa）
|
Not recorded | CL CHLORIDE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.58 Å |
| 9IGJ structure of two human ELF2 transcription factors in complex with a nucleosome Deposited 2025-02-19 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；1 mM EDTA, 30 mM NaCl, 2 mM DTT in 20 mM HEPES, pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 9IHD Nucleosome core particle bound by one molecule of DTT-reduced native monomeric myeloperoxidase Deposited 2025-02-21 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain D
30–125（96 aa）
Chain H
30–125（96 aa）
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.97 Å |
| 9IHE Nucleosome core particle bound by two molecules of DTT-reduced native monomeric myeloperoxidase Deposited 2025-02-21 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
Chain D
30–125（96 aa）
Chain H
30–125（96 aa）
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.95 Å |
| 9IHF Nucleosome core particle bound by one monomer and one dimer of of DTT-reduced native myeloperoxidase Deposited 2025-02-21 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric（16） Review required |
Chain D
30–125（96 aa）
Chain H
30–125（96 aa）
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 9JAO The structure of SMARCAD1 bound to the hexasome in the presence of ADP-BeFx Deposited 2024-08-25 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain H
5–126（122 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9M76 UHRF1 bound to a mononucleosome in its pre-active state, with the RING domain bound to the SRA domain. Deposited 2025-03-09 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | ZN ZINC ION × 5 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 9M77 The activated state of human UHRF1 bound to a mononucleosome, with the finger loop ordered and linker 4 disordered. Deposited 2025-03-09 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | ZN ZINC ION × 3 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 9MPP The cryo-EM structure of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L Deposited 2024-12-31 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 6 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9N6H 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex Deposited 2025-02-05 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
33–126（94 aa）
Chain H
33–126（94 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.54 Å |
| 9N6I 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex Deposited 2025-02-05 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain D
33–126（94 aa）
Chain H
33–126（94 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.61 Å |
| 9NH8 CHD1-nucleosome complex (anchored state) Deposited 2025-02-24 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ARG ARGININE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9NY4 USP21 bound to H2AK119ub nucleosome Deposited 2025-03-26 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 9Q7U Composite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer bound to 167H3K36me2-nucleosome Deposited 2025-08-25 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 9 SAO 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9QAJ Structure of the nucleosome-bound human BCL7A Deposited 2025-02-28 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.95 Å |
| 9QIK M2 nucleosome Deposited 2025-03-17 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain C
1–126（126 aa）
Chain D
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.03 Å |
| 9R5K Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-09 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20mM Hepes, 120mM Nacl
cryo-EM vitrification conditions
Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity
|
Resolution 4.20 Å |
| 9R5S Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-09 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20mM Hepes, 120mM Nacl
cryo-EM vitrification conditions
Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity
|
Resolution 3.80 Å |
| 9R5W Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-10 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20mM Hepes, 120mM Nacl
cryo-EM vitrification conditions
Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity
|
Resolution 3.80 Å |
| 9T4V ALC1/CHD1L in an intermediate conformation, bound to a PARylated nucleosome Deposited 2025-11-02 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；3 uL were applied on grid and immediately blotted for 2.5 s at blot force 0.
|
Resolution 6.60 Å |
| 9W74 Cryo-EM structure of the close-packed di-hexasome (CPDH) Deposited 2025-08-05 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain N
5–126（122 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.94 Å |
| 9WBZ The structure of NCP-motor-ARP module of ncBAF-nucleosome complex Deposited 2025-08-15 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9WC0 The structure of NCP-RA module of ncBAF-nucleosome complex Deposited 2025-08-15 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å |
| 9XYC Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome LEDGF+nucleosome map Q Deposited 2025-08-25 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain d
1–126（126 aa）
Chain h
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9Y4P Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker Deposited 2025-09-03 | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain D
5–126（122 aa）
Chain H
5–126（122 aa）
Chain P
5–126（122 aa）
Chain T
5–126（122 aa）
|
Not recorded | ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.84 Å |