Histone H3.2
Xenopus laevis
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein–DNA Heteromer Protein × 12 DNA 2 PDB declaration: 14-meric（14） Consistent with all polymer counts | Chain A； UniProt 2–136 Chain E； UniProt 2–136 | Not recorded | Histone H4 × 2 （P62799） Histone H2A type 1 × 2 （P06897） Histone H2B 1.1 × 2 （P02281） DNA (167-MER) × 1 DNA (167-MER) × 1 DNA (cytosine-5)-methyltransferase 3A × 2 （Q9Y6K1） DNA (cytosine-5)-methyltransferase 3-like × 2 （Q9UJW3） 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 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 9MPP | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1KX3 X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution Deposited 2002-01-31 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–135（135 aa）
Chain E
1–135（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.275 |
| 1ZBB Structure of the 4_601_167 Tetranucleosome Deposited 2005-04-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 36-meric |
Chain A
1–135（135 aa）
Chain E
1–135（135 aa）
Chain a
1–135（135 aa）
Chain e
1–135（135 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.75；294 K；magnesium chloride, potassium chloride, potassium cacodylate, trisCl, pH 6.75, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 9.00 Å |
| 2F8N 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes Deposited 2005-12-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–135（135 aa）
Chain E
1–135（135 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；34 to 37.5mM KCl and 40-45mM MnCl2, 5mM Potassium Cacodylate, Sample concentration: 8-12 mg/ml, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.90 Å R-free 0.269 |
| 2IO5 Crystal structure of the CIA- histone H3-H4 complex Deposited 2006-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–135（135 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M HEPES, 0.05M cadmium sulfate hydrate, 1.0M sodium acetate tryhydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.70 Å R-free 0.293 |
| 3B6F Nucleosome core particle treated with cisplatin Deposited 2007-10-29 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K
|
Resolution 3.45 Å R-free 0.402 |
| 3B6G Nucleosome core particle treated with oxaliplatin Deposited 2007-10-29 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；MnCl2, KCl, K-Cacodylate, pH 6.0, vapor diffusion, temperature 291K
|
Resolution 3.45 Å R-free 0.435 |
| 3KUY DNA Stretching in the Nucleosome Facilitates Alkylation by an Intercalating Antitumor Agent Deposited 2009-11-28 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 ATV 2-[(2R)-oxiran-2-ylmethyl]-1H-benzo[de]isoquinoline-1,3(2H)-dione × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 6；291 K；85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, EVAPORATION
|
Resolution 2.90 Å R-free 0.286 |
| 3KWQ Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Deposited 2009-12-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
39–136（98 aa）
Fragment：UNP residues 39-136
Chain E
39–136（98 aa）
Fragment：UNP residues 39-136
|
Mutation：K57E Mutation：K57E | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.50 Å R-free 0.315 |
| 3KXB Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Deposited 2009-12-02 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：K57E, G103A Mutation：K57E, G103A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；Crystals were grown by vapor diffusion in 8 20 days at 20 C using a droplet containing 4.0 mg ml−1 core particle 50 mM KCl, 70 75 mM MnCl , and 20 mM potassium cacodylate, pH 6.0, surrounded by silicon oil DC200 (110mPa s; Fluka) and equilibrated against 40 46 mM MnCl2, 35 40 mM KCl and 20 mM potassium cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 293K
|
Resolution 3.20 Å R-free 0.292 |
| 3LEL Structural Insight into the Sequence-Dependence of Nucleosome Positioning Deposited 2010-01-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 15 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85mM MnCl2, 60mM KCl, 20mM K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.95 Å R-free 0.300 |
| 3LEL Structural Insight into the Sequence-Dependence of Nucleosome Positioning Deposited 2010-01-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 19 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85mM MnCl2, 60mM KCl, 20mM K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.95 Å R-free 0.300 |
| 3LJA Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome Deposited 2010-01-26 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 45 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；85 mM MnCl2, 60 mM KCl, 20 mM K-Cacodylate, 4 mg/ml NCP over well with 1/2 conc., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, EVAPORATION
|
Resolution 2.75 Å R-free 0.259 |
| 3LZ0 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 1) Deposited 2010-03-01 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K cacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.50 Å R-free 0.318 |
| 3LZ1 Crystal Structure of Nucleosome Core Particle Composed of the Widom 601 DNA Sequence (orientation 2) Deposited 2010-03-01 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；Kcacodylate, KCl, MnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.50 Å R-free 0.319 |
| 3MGP Binding of Cobalt ions to the Nucleosome Core Particle Deposited 2010-04-07 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | CL CHLORIDE ION × 4 CO COBALT (II) ION × 43 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 2.44 Å R-free 0.282 |
| 3MGQ Binding of Nickel ions to the Nucleosome Core Particle Deposited 2010-04-07 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | NI NICKEL (II) ION × 47 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 2.65 Å R-free 0.276 |
| 3MGR Binding of Rubidium ions to the Nucleosome Core Particle Deposited 2010-04-07 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | CL CHLORIDE ION × 4 RB RUBIDIUM ION × 5 MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 2.30 Å R-free 0.267 |
| 3MGS Binding of Cesium ions to the Nucleosome Core particle Deposited 2010-04-07 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | CL CHLORIDE ION × 4 CS CESIUM ION × 12 MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；85mM MnCl2, 60mM KCl, 40mM K-cacodylate , pH 6.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 3.15 Å R-free 0.238 |
| 3MNN A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core Deposited 2010-04-22 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RU RUTHENIUM ION × 3 MML 1-methyl-4-(1-methylethyl)benzene × 3 PTW 1,3,5-triaza-7-phosphatricyclo[3.3.1.1~3,7~]decane × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；55mM KCl, 85mM MnCl2, 20mM K-Cacodylate, pH 6, VAPOR DIFFUSION, temperature 291K
|
Resolution 2.50 Å R-free 0.277 |
| 3MVD Crystal structure of the chromatin factor RCC1 in complex with the nucleosome core particle Deposited 2010-05-04 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；294 K；25 mM sodium acetate buffer, 25 mM sodium citrate, 1 mM DTT, 6 % PEG2000-MME, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 2.90 Å R-free 0.215 |
| 3O62 Nucleosome core particle modified with a cisplatin 1,3-cis-{Pt(NH3)2}2+-d(GpTpG) intrastrand cross-link Deposited 2010-07-28 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | CPT Cisplatin × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；40-46 mM MnCl2, 30-45 mM KCl, and 20 mM potassium cacodylate pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 3.22 Å R-free 0.306 |
| 3REH 2.5 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Deposited 2011-04-04 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 15 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；KCl, MnCl2, K-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.50 Å R-free 0.270 |
| 3REI 2.65 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 145 bp Alpha-Satellite DNA (NCP145) Derivatized with Triamminechloroplatinum(II) Chloride Deposited 2011-04-04 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | PT PLATINUM (II) ION × 49 SO4 SULFATE ION × 3 MN MANGANESE (II) ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.65 Å R-free 0.276 |
| 3REJ 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Deposited 2011-04-04 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 13 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.55 Å R-free 0.262 |
| 3REK 2.6 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Oxaliplatin Deposited 2011-04-04 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 PT PLATINUM (II) ION × 40 SO4 SULFATE ION × 3 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.60 Å R-free 0.281 |
| 3REL 2.7 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with a 146 bp Alpha-Satellite DNA (NCP146b) Derivatized with Triamminechloroplatinum(II) Chloride Deposited 2011-04-04 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 PT PLATINUM (II) ION × 48 SO4 SULFATE ION × 3 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.70 Å R-free 0.302 |
| 3TU4 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Deposited 2011-09-15 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
Resolution 3.00 Å R-free 0.241 |
| 3TU4 Crystal structure of the Sir3 BAH domain in complex with a nucleosome core particle. Deposited 2011-09-15 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
Resolution 3.00 Å R-free 0.241 |
| 3UT9 Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601' Derivative (NCP-601L) Deposited 2011-11-25 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 29 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.20 Å R-free 0.289 |
| 3UTA Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence Containing Two TTAAA elements (NCP-TA2) Deposited 2011-11-25 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 17 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.07 Å R-free 0.266 |
| 3UTB Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite Sequence (NCP146b) Deposited 2011-11-25 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 21 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；K-cacodylate, KCl, MnCl2, pH 6.0, temperature 291K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.20 Å R-free 0.275 |
| 4EO5 Yeast Asf1 bound to H3/H4G94P mutant Deposited 2012-04-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
62–136（75 aa）
Fragment：residues 60-135
|
Mutation：G102A | ACT ACETATE ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.9；298 K；7.14% PEG 3350, 0.2 M Magnesium Acetate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.35 Å R-free 0.240 |
| 4J8U X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)osmium(II) Deposited 2013-02-15 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SO4 SULFATE ION × 3 ELJ chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)osmium(II) × 3 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.38 Å R-free 0.280 |
| 4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric |
Chain A
2–136（135 aa）
|
Not recorded | SO4 SULFATE ION × 1 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.58 Å R-free 0.273 |
| 4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric |
Chain E
2–136（135 aa）
|
Not recorded | SO4 SULFATE ION × 2 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.58 Å R-free 0.273 |
| 4J8V X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-phenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SO4 SULFATE ION × 3 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.58 Å R-free 0.273 |
| 4J8W X-ray structure of NCP145 with chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) Deposited 2013-02-15 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SO4 SULFATE ION × 3 1MK chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)osmium(II) × 3 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.41 Å R-free 0.275 |
| 4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric |
Chain A
2–136（135 aa）
|
Not recorded | SO4 SULFATE ION × 1 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.87 Å R-free 0.280 |
| 4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: pentameric |
Chain E
2–136（135 aa）
|
Not recorded | SO4 SULFATE ION × 2 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.87 Å R-free 0.280 |
| 4J8X X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II) Deposited 2013-02-15 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SO4 SULFATE ION × 3 RU7 PARA-CYMENE RUTHENIUM CHLORIDE × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.87 Å R-free 0.280 |
| 4KGC Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM Deposited 2013-04-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | HRU (ethane-1,2-diamine-kappa~2~N,N')[(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)cyclohexane-1,2,3,4,5,6-hexayl]ruthenium × 4 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.69 Å R-free 0.282 |
| 4LD9 Crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle Deposited 2013-06-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；293.15 K；50 mM MES pH 6.5, 12% PEG 400, 12 mM MnCl2, 100 mM NaCl, 10 mM EDTA, VAPOR DIFFUSION, temperature 293.15K
|
Resolution 3.31 Å R-free 0.295 |
| 4R8P Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle Deposited 2014-09-02 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
Modified micro batch under oil；pH 7.5；294 K；25 mM HEPES pH 7.5, 80 mM NH4NO3, 3 % PEG2000-MME, Modified micro batch under oil, temperature 294K
|
Resolution 3.28 Å R-free 0.245 |
| 4WU8 Structure of trPtNAP-NCP145 Deposited 2014-10-31 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：G102A Mutation：G102A | CX3 [2-(3-{bis[2-(amino-kappaN)ethyl]amino-kappaN}propyl)-1H-benzo[de]isoquinoline-1,3(2H)-dionato(2-)]platinum(1+) × 2 SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Manganese chloride, potassium chloride, potassium cacodylate
|
Resolution 2.45 Å R-free 0.263 |
| 4WU9 Structure of cisPtNAP-NCP145 Deposited 2014-10-31 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：G102A Mutation：G102A | SO4 SULFATE ION × 2 MG MAGNESIUM ION × 1 CX8 [2-{3-[(2-{[2-(amino-kappaN)ethyl]amino-kappaN}ethyl)amino-kappaN]propyl}-1H-benzo[de]isoquinoline-1,3(2H)-dionato(3-)]platinum × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Manganese chloride, potassium chloride, potassium cacodylate
|
Resolution 2.60 Å R-free 0.273 |
| 4XUJ Nucleosome core particle containing adducts from treatment with a thiomorpholine-substituted [(eta-6-p-cymene)Ru(3-hydroxy-2-pyridone)Cl] compound Deposited 2015-01-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Fragment：UNP residues 2-136
Chain E
2–136（135 aa）
Fragment：UNP residues 2-136
|
Not recorded | SO4 SULFATE ION × 3 4A6 [(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)benzene]ruthenium × 3 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40mM MnCl2, 30mM KCl, 20mM K-Cacodylate
|
Resolution 3.18 Å R-free 0.299 |
| 4XZQ Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-02-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
39–136（98 aa）
Fragment：residues 39-136
Chain E
39–136（98 aa）
Fragment：residues 39-136
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292.15 K；potassium chloride, potassium cacodylate, manganese chloride
|
Resolution 2.40 Å R-free 0.299 |
| 4YS3 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
39–136（98 aa）
Fragment：residues 39-136
Chain E
39–136（98 aa）
Fragment：residues 39-136
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.9；292.15 K；postassium chloride, manganese chloride, cacodylate
|
Resolution 3.00 Å R-free 0.279 |
| 4Z66 Nucleosome disassembly by RSC and SWI/SNF is enhanced by H3 acetylation near the nucleosome dyad axis Deposited 2015-04-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
39–136（98 aa）
Chain E
39–136（98 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292.15 K；potassium chloride, potassium cacodylate, manganese chloride
|
Resolution 2.50 Å R-free 0.296 |
| 4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 16 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
|
Resolution 3.82 Å R-free 0.256 |
| 4ZUX SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome Deposited 2015-05-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric |
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 16 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Tris-acetate pH 7.4, 50 mM sodium acetate, 5 mM Mg-acetate, 5% sucrose and 5% 2-propanol
|
Resolution 3.82 Å R-free 0.256 |
| 5BS7 Structure of histone H3/H4 in complex with Spt2 Deposited 2015-06-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
26–136（111 aa）
Fragment：residues 26-136
Chain B
26–136（111 aa）
Fragment：residues 26-136
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；0.02 M NaCl, 0.2 M HEPES 7.5, 1.5 M ammonium sulfate
|
Resolution 3.30 Å R-free 0.290 |
| 5BSA Structure of histone H3/H4 in complex with Spt2 Deposited 2015-06-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
27–136（110 aa）
Fragment：residues 27-136
Chain B
27–136（110 aa）
Fragment：residues 27-136
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；0.02 M NaCl, 0.2 M HEPES 7.5, 1.6 M ammonium sulfate
|
Resolution 4.61 Å R-free 0.329 |
| 5CP6 Nucleosome Core Particle with Adducts from the Anticancer Compound, [(eta6-5,8,9,10-tetrahydroanthracene)Ru(ethylenediamine)Cl][PF6] Deposited 2015-07-21 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | RUH (ethane6-5,8,9,10-tetrahydroanthracene)Ru(II)(ethylene-diamine)Cl × 3 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.60 Å R-free 0.251 |
| 5DNM Nucleosome core particle containing adducts of ruthenium(II)-toluene PTA complex Deposited 2015-09-10 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RAX dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate
|
Resolution 2.81 Å R-free 0.241 |
| 5DNN Nucleosome core particle containing adducts of gold(I)-triethylphosphane and ruthenium(II)-toluene PTA complexes Deposited 2015-09-10 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | AUF triethylphosphanuidylgold(1+) × 2 SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RAX dichloro[(1,2,3,4,5,6-eta)-6-methylbenzene]1,3,5-triaza-7lambda~5~-phosphatricyclo[3.3.1.1~3,7~]dec-7-ylruthenium × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate
|
Resolution 2.80 Å R-free 0.236 |
| 5E5A Crystal structure of the chromatin-tethering domain of Human cytomegalovirus IE1 protein bound to the nucleosome core particle Deposited 2015-10-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.2；289 K；sodium cacodylate, magnesium
acetate, 2-methyl-2,4-pentanediol
|
Resolution 2.81 Å R-free 0.242 |
| 5F99 X-ray Structure of the MMTV-A Nucleosome Core Particle Deposited 2015-12-09 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：C110A Mutation：C110A | CL CHLORIDE ION × 4 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；sample was mixed 1:1 with 10 mM K-cacodylate, pH 6.0, 180 mM MgCl2, 50 mM KCl and equilibrated against a 1:4 dilution of the same solution
|
Resolution 2.63 Å R-free 0.252 |
| 5HQ2 Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle Deposited 2016-01-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: hexadecameric |
Chain A
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 5.5；277 K；25 mM sodium acetate pH 5.5, 40 mM sodium citrate,1 mM DTT, 6% PEG2000-MME
|
Resolution 4.50 Å R-free 0.397 |
| 5KGF Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution Deposited 2016-06-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；High concentration NCP-ubme/GST-53BP1 complex at 200 mM salt was diluted just prior to grid freezing.
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE；Plunged into liquid ethane-propane (FEI VITROBOT MARK III)
|
Resolution 4.54 Å |
| 5MLU Crystal structure of the PFV GAG CBS bound to a mononucleosome Deposited 2016-12-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
40–136（97 aa）
Chain E
40–136（97 aa）
|
Not recorded | MN MANGANESE (II) ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.05M MnCl2, 0.04M KCl, 0.1M potassium cacodylate pH 6.0, 5% trehalose, 24% MPD
|
Resolution 2.80 Å R-free 0.252 |
| 5NL0 Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1 Deposited 2017-04-03 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；293.15 K；Mix of equal volumes of the nucleosome/H1 complex (25-30 microM) and a crystallization solution composed of MPD (6% v/v), 50 mM NaCl, and 50 mM sodium potassium phosphate pH 6.4.
|
Resolution 5.40 Å R-free 0.265 |
| 5NL0 Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1 Deposited 2017-04-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric |
Chain K
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；293.15 K；Mix of equal volumes of the nucleosome/H1 complex (25-30 microM) and a crystallization solution composed of MPD (6% v/v), 50 mM NaCl, and 50 mM sodium potassium phosphate pH 6.4.
|
Resolution 5.40 Å R-free 0.265 |
| 5O9G Structure of nucleosome-Chd1 complex Deposited 2017-06-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 5OMX X-ray Structure of the H2A-N38C Nucleosome Core Particle Deposited 2017-08-02 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：C110A Mutation：C110A | MN MANGANESE (II) ION × 33 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；8 mg/ml sample was mixed 1:1 with 10 mM K-Cacodylate (pH 6.0), 140-150 mM MnCl2, 100 KCl. and equilibrated against a 1:4 dilution of the same solution
|
Resolution 2.32 Å R-free 0.259 |
| 5ONG X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer Deposited 2017-08-03 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：C110A, R40C Mutation：C110A, R40C | MN MANGANESE (II) ION × 20 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；Sample was mixed in a 1:1 ratio with 10 mM Na-cacodylate, pH 6.0, 130-180 mM MnCl2, 100-160 mM KCl and equilibrated against a 1:4 dilution of the same solution
|
Resolution 2.80 Å R-free 0.247 |
| 5ONW X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two H2A/H2B dimers crosslinked via H2A N38C Deposited 2017-08-04 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：C110A, R40C Mutation：C110A, R40C | MN MANGANESE (II) ION × 20 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；Sample was mixed in a 1:1 ratio with 10 mM Na-cacodylate, pH 6.0, 160-210 mM MnCl2, 140-200 mM KCl and equilibrated against a 1:4 dilution of the same solution
|
Resolution 2.80 Å R-free 0.254 |
| 5OXV Structure of the 4_601_157 tetranucleosome (C2 form) Deposited 2017-09-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
Chain K
2–136（135 aa）
Chain O
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；291 K；30-60 mM KCl, 90-110 mM MgCl2 and 5 mM Na-cacodylate, pH 6
|
Resolution 6.72 Å R-free 0.352 |
| 5X0X Complex of Snf2-Nucleosome complex with Snf2 bound to position +6 of the nucleosome Deposited 2017-01-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.97 Å |
| 5X0Y Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome Deposited 2017-01-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.69 Å |
| 5XF6 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker Deposited 2017-04-07 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SO4 SULFATE ION × 3 MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 EDN ETHANE-1,2-DIAMINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate , pH 6.0
|
Resolution 2.63 Å R-free 0.254 |
| 5Z3L Structure of Snf2-nucleosome complex in apo state Deposited 2018-01-08 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.31 Å |
| 5Z3O Structure of Snf2-nucleosome complex in ADP state Deposited 2018-01-08 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.62 Å |
| 5Z3U Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state Deposited 2018-01-08 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.31 Å |
| 5Z3V Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state Deposited 2018-01-08 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.22 Å |
| 6ESF Nucleosome : Class 1 Deposited 2017-10-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 6ESG Nucleosome breathing : Class 2 Deposited 2017-10-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.40 Å |
| 6ESH Nucleosome breathing : Class 3 Deposited 2017-10-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.10 Å |
| 6ESI Nucleosome breathing : Class 4 Deposited 2017-10-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.30 Å |
| 6I84 Structure of transcribing RNA polymerase II-nucleosome complex Deposited 2018-11-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric |
Chain M
1–136（136 aa）
Chain S
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 6JM9 cryo-EM structure of DOT1L bound to unmodified nucleosome Deposited 2019-03-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
39–136（98 aa）
Chain E
39–136（98 aa）
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.30 Å |
| 6JMA cryo-EM structure of DOT1L bound to H2B ubiquitinated nucleosome Deposited 2019-03-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
39–136（98 aa）
Chain E
39–136（98 aa）
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.80 Å |
| 6KW3 The ClassA RSC-Nucleosome Complex Deposited 2019-09-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric |
Chain N
1–136（136 aa）
Chain Q
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.13 Å |
| 6KW4 The ClassB RSC-Nucleosome Complex Deposited 2019-09-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric |
Chain N
1–136（136 aa）
Chain Q
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.55 Å |
| 6KW5 The ClassC RSC-Nucleosome Complex Deposited 2019-09-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric |
Chain R
1–136（136 aa）
Chain V
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 10.13 Å |
| 6NE3 Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at SHL-2 Deposited 2018-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G102A Mutation：G102A | ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；2.5 ul of nucleosome-443 SNF2h complexes were applied to a glow discharged Quantifoil holey carbon grid (1.2 um hole size, 400 mesh), blotted in a Vitrobot Mark I (FEI Company) using 6 seconds blotting at 100% humidity, and then plunge-frozen in liquid ethane cooled by liquid nitrogen.
|
Resolution 3.90 Å |
| 6NJ9 Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex Deposited 2019-01-02 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：G102A, K79Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：G102A, K79Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) | SAM S-ADENOSYLMETHIONINE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions
Cryogen ETHANE；Blot once for 3.5 seconds before freezing.
|
Resolution 2.96 Å |
| 6NN6 Structure of Dot1L-H2BK120ub nucleosome complex Deposited 2019-01-14 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：G103A Mutation：G103A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 6NOG Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome Deposited 2019-01-16 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：G102A Mutation：G102A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions
Cryogen ETHANE；Blot once for 3.5 seconds before freezing
|
Resolution 3.90 Å |
| 6NQA Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex Deposited 2019-01-19 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：G102A, K79Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：G102A, K79Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) | SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions
Cryogen ETHANE；Blot once for 3.5 seconds before freezing.
|
Resolution 3.54 Å |
| 6O22 Structure of Asf1-H3:H4-Rtt109-Vps75 histone chaperone-lysine acetyltransferase complex with the histone substrate. Deposited 2019-02-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
Experimental method not declared
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition
70 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 70 uM Rtt109, 70 uM Asf1, 70 uM H3, 70 uM H4, 100% D2O | 100% D2O
NMR sample composition
70 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 70 uM Rtt109, 70 uM Asf1, 70 uM H3(110A,63C) mutant with a cysteine coupled to a paramagnetic tag, 70 uM H4, 100% D2O | 100% D2O
NMR sample composition
90 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 90 uM Rtt109, 90 uM Asf1, 90 uM H3(110A,76C) mutant with a cysteine coupled to a paramagnetic tag, 90 uM H4, 100% D2O | 100% D2O
NMR sample composition
30 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 30 uM Rtt109, 30 uM Asf1, 30 uM H3, 30 uM H4(30C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2O | 100% D2O
NMR sample composition
70 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 70 uM Rtt109, 70 uM Asf1, 70 uM H3, 70 uM H4(82C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2O | 100% D2O
NMR sample composition
80 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 80 uM Rtt109, 80 uM Asf1, 80 uM H3, 80 uM H4(45C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2O | 100% D2O
NMR sample composition
30 uM ILV methyl labelled, perdeuterated Vps75 (dimer), 30 uM Rtt109, 30 uM Asf1, 30 uM H3, 30 uM H4(93C) mutant with a cysteine coupled to a paramagnetic tag, 100% D2O | 100% D2O
|
Resolution not provided |
| 6O96 Dot1L bound to the H2BK120 Ubiquitinated nucleosome Deposited 2019-03-13 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：G102A Mutation：G102A | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen PROPANE；blotted for 3s before plunging
|
Resolution 3.50 Å |
| 6OM3 Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle Deposited 2019-04-18 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：G102A Mutation：G102A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；277.15 K；6 mM Na-Cacodylate pH 6.0, 0.4 mM Spermine-HCl, 2 mM MgCl2 and 1.75% v/v PEG 400
|
Resolution 3.30 Å R-free 0.250 |
| 6OM3 Crystal structure of the Orc1 BAH domain in complex with a nucleosome core particle Deposited 2019-04-18 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain M
2–136（135 aa）
Chain Q
2–136（135 aa）
|
Mutation：G102A Mutation：G102A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；277.15 K；6 mM Na-Cacodylate pH 6.0, 0.4 mM Spermine-HCl, 2 mM MgCl2 and 1.75% v/v PEG 400
|
Resolution 3.30 Å R-free 0.250 |
| 6PA7 The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome. Deposited 2019-06-11 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | CL CHLORIDE ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 6PWV Cryo-EM structure of MLL1 core complex bound to the nucleosome Deposited 2019-07-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
Chain G
1–136（136 aa）
Chain K
1–136（136 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.20 Å |
| 6PWW Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome Deposited 2019-07-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain G
1–136（136 aa）
Chain K
1–136（136 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 6PWX Cryo-EM structure of RbBP5 bound to the nucleosome Deposited 2019-07-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain G
1–136（136 aa）
Chain K
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 6R1U Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2 Deposited 2019-03-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.36 Å |
| 6RYR Nucleosome-CHD4 complex structure (single CHD4 copy) Deposited 2019-06-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 6RYU Nucleosome-CHD4 complex structure (two CHD4 copies) Deposited 2019-06-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 6T9L SAGA DUB module bound to a ubiqitinated nucleosome Deposited 2019-10-28 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 4 seconds before plunging
|
Resolution 3.60 Å |
| 6TDA Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome Deposited 2019-11-08 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 15.00 Å |
| 6UXW SWI/SNF nucleosome complex with ADP-BeFx Deposited 2019-11-08 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric |
Chain R
2–136（135 aa）
Chain V
2–136（135 aa）
|
Not recorded | PO4 PHOSPHATE ION × 12 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；10 mM HEPES, pH 7.9, 10 mM MgCl2, 50 mM KCl, 1 mM DTT, 5% glycerol, 0.05% NP-40
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.96 Å |
| 6VEN Yeast COMPASS in complex with a ubiquitinated nucleosome Deposited 2020-01-02 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：K4(NLE), M90(NLE), M120(NLE), G102A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K4(NLE), M90(NLE), M120(NLE), G102A Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot force 5
3.5 sec blot time
|
Resolution 3.37 Å |
| 6W5I Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class01) Deposited 2020-03-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain G
1–136（136 aa）
Chain K
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.90 Å |
| 6W5M Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class02) Deposited 2020-03-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain G
1–136（136 aa）
Chain K
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 6W5N Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05) Deposited 2020-03-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain G
1–136（136 aa）
Chain K
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.00 Å |
| 6WKR PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome Deposited 2020-04-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: octadecameric |
Chain I
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 6WZ5 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.20 Å |
| 6WZ9 Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-13 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 6X0N Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 23-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
Chain a
2–136（135 aa）
Chain e
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 10.00 Å |
| 6Z6P HDAC-PC-Nuc Deposited 2020-05-28 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain E
40–136（97 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.43 Å |
| 7AT8 Histone H3 recognition by nucleosome-bound PRC2 subunit EZH2. Deposited 2020-10-29 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain D
2–136（135 aa）
Chain H
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 7 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 4.40 Å |
| 7EG6 Snf5 Finger Helix bound to the nucleosome Deposited 2021-03-24 | Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7EGP The structure of SWI/SNF-nucleosome complex Deposited 2021-03-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric |
Chain O
2–136（135 aa）
Chain S
2–136（135 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.90 Å |
| 7ENN The structure of ALC1 bound to the nucleosome Deposited 2021-04-18 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7K6P Active state Dot1 bound to the unacetylated H4 nucleosome Deposited 2020-09-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
38–135（98 aa）
Chain E
38–135（98 aa）
|
Mutation：K79M, G103A Mutation：K79M, G103A | SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7K6Q Active state Dot1 bound to the H4K16ac nucleosome Deposited 2020-09-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
38–135（98 aa）
Chain E
38–135（98 aa）
|
Mutation：K79M, G103A Mutation：K79M, G103A | SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7KBD Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction) Deposited 2020-10-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.38 Å |
| 7KBE Nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction) Deposited 2020-10-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7KBF H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction) Deposited 2020-10-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.42 Å |
| 7NKX RNA polymerase II-Spt4/5-nucleosome-Chd1 structure Deposited 2021-02-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7NKY RNA Polymerase II-Spt4/5-nucleosome-FACT structure Deposited 2021-02-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 27-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7OH9 Nucleosome with TBP and TFIIA bound at SHL -6 Deposited 2021-05-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7OHA nucleosome with TBP and TFIIA bound at SHL +2 Deposited 2021-05-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7OHB TBP-nucleosome complex Deposited 2021-05-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7OHC Cryo-EM structure of nucleosome core particle composed of the Widom 601 DNA sequence Deposited 2021-05-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 7OTQ Cryo-EM structure of ALC1/CHD1L bound to a PARylated nucleosome Deposited 2021-06-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：C110A Mutation：C110A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；3 uL were applied on grid and immediately blotted for 2.5 s at blot force 0.
|
Resolution 4.80 Å |
| 7SSA Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome Deposited 2021-11-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7UNC Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome Deposited 2022-04-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 29 PDB declaration: 32-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Mutation：G102A Mutation：G102A | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7UND Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) Deposited 2022-04-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Mutation：G102A Mutation：G102A | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7XFC Structure of nucleosome-DI complex (-30I, Apo state) Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.90 Å |
| 7XFH Structure of nucleosome-AAG complex (A-30I, post-catalytic state) Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.90 Å |
| 7XFI Structure of nucleosome-DI complex (-50I, Apo state) Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.90 Å |
| 7XFJ Structure of nucleosome-AAG complex (T-50I, post-catalytic state) Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 3.00 Å |
| 7XFL Structure of nucleosome-AAG complex (A-53I, free state) Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.80 Å |
| 7XFM Structure of nucleosome-AAG complex (A-53I, post-catalytic state) Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 3.10 Å |
| 7XFN Structure of nucleosome-DI complex (-55I, Apo state) Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.80 Å |
| 7XNP Structure of nucleosome-AAG complex (A-55I, post-catalytic state) Deposited 2022-04-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.90 Å |
| 7YRD histone methyltransferase Deposited 2022-08-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
34–136（103 aa）
Chain E
34–136（103 aa）
|
Mutation：G2E,G70A Mutation：G2E,G70A | ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7YRG histone methyltransferase Deposited 2022-08-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
34–136（103 aa）
Chain E
34–136（103 aa）
|
Mutation：G2E,G70A Mutation：G2E,G70A | ZN ZINC ION × 2 SAM S-ADENOSYLMETHIONINE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06 | Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric |
Chain a
2–136（135 aa）
Chain e
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric |
Chain a
2–136（135 aa）
Chain e
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric |
Chain a
2–136（135 aa）
Chain e
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.60 Å |
| 8A3Y Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex Deposited 2022-06-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 27 PDB declaration: 30-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Mutation：G103A Mutation：G103A | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Mutation：G103A Mutation：G103A | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8BZ1 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Deposited 2022-12-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Mutation：G103A Mutation：G103A | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8CEO Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Deposited 2023-02-02 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric |
Chain r
2–136（135 aa）
Chain v
2–136（135 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8F86 SIRT6 bound to an H3K9Ac nucleosome Deposited 2022-11-21 | Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ZSL [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3aR,5R,6R,6aR)-6-hydroxytetrahydro-2H-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8G6Q H2AK119ub-modified nucleosome ubiquitin position 1 Deposited 2023-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G102A Mutation：G102A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.41 Å |
| 8G6S H2AK119ub-modified nucleosome ubiquitin position 2 Deposited 2023-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G102A Mutation：G102A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.47 Å |
| 8G86 Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of nucleosome) Deposited 2023-02-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 8G88 Human Oct4 bound to nucleosome with human nMatn1 sequence Deposited 2023-02-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 8G8B Nucleosome with human nMatn1 sequence in complex with Human Oct4 Deposited 2023-02-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 8G8G Interaction of H3 tail in LIN28B nucleosome with Oct4 Deposited 2023-02-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50 mM HEPES pH 7.5, 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8GPN Human menin in complex with H3K79Me2 nucleosome Deposited 2022-08-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K79 dimethylation Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K79 dimethylation Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8OF4 Nucleosome Bound human SIRT6 (Composite) Deposited 2023-03-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 8RUP Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome Deposited 2024-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric |
Chain A
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blotting time, -10 force, no wait time.
|
Resolution 2.42 Å |
| 8RUQ Borealin N-terminus in complex with H3.T3p-nucleosome Deposited 2024-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blotting time, -10 force, no wait time.
|
Resolution 2.29 Å |
| 8SIY Origin Recognition Complex Associated (ORCA) protein bound to H4K20me3-nucleosome Deposited 2023-04-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain C
2–136（135 aa）
Chain G
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8SKZ Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome Deposited 2023-04-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric |
Chain B
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8SVF BAP1/ASXL1 bound to the H2AK119Ub Nucleosome Deposited 2023-05-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G103A Mutation：G103A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8T3T Structure of Bre1-nucleosome complex - state3 Deposited 2023-06-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.21 Å |
| 8T3W Structure of Bre1-nucleosome complex - state2 Deposited 2023-06-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 8T3Y Structure of Bre1-nucleosome complex - state1 Deposited 2023-06-08 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM HEPES, pH 7.5, 50 mM NaCl, 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.47 Å |
| 8T9F Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Deposited 2023-06-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 8T9G Automethylated PRC2 dimer bound to nucleosome Deposited 2023-06-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric |
Chain A
1–136（136 aa）
Chain W
1–136（136 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.20 Å |
| 8T9H Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Deposited 2023-06-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.37 Å |
| 8TAS PRC2 monomer bound to nucleosome Deposited 2023-06-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric |
Chain I
1–136（136 aa）
Chain W
1–136（136 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8TB9 PRC2-J119-450 monomer bound to H1-nucleosome Deposited 2023-06-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric |
Chain I
1–136（136 aa）
Chain W
1–136（136 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8THU Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 Deposited 2023-07-18 | Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8UW1 Cryo-EM structure of DNMT3A1 UDR in complex with H2AK119Ub-nucleosome Deposited 2023-11-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9；50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.88 Å |
| 8UXQ Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome Deposited 2023-11-09 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric |
Chain E
2–136（135 aa）
Chain K
2–136（135 aa）
|
Mutation：C110A Mutation：C110A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.30 Å |
| 8V25 H2BK120ub-modified nucleosome ubiquitin position 1 Deposited 2023-11-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G102A Mutation：G102A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 8V26 H2BK120ub-modified nucleosome ubiquitin position 2 Deposited 2023-11-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G102A Mutation：G102A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.33 Å |
| 8V27 H2BK120ub-modified nucleosome ubiquitin position 3 Deposited 2023-11-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G102A Mutation：G102A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.34 Å |
| 8V28 H2BK120ub-modified nucleosome ubiquitin position 4 Deposited 2023-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G102A Mutation：G102A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.36 Å |
| 8V4Y Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 1) Deposited 2023-11-29 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：G102A, C110A Mutation：G102A, C110A | ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8V6V Cryo-EM structure of doubly-bound SNF2h-nucleosome complex Deposited 2023-12-03 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：G102A, C110A Mutation：G102A, C110A | ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8V7L Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 2) Deposited 2023-12-04 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：G102A, C110A Mutation：G102A, C110A | ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8VX5 Nucleosome core particle containing an 8-oxoG damage site Deposited 2024-02-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G102A Mutation：G102A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8VX6 Human OGG1 bound at the nucleosomal DNA entry site Deposited 2024-02-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G102A Mutation：G102A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9B2S Haspin bound to nucleosome in position 1 Deposited 2024-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G102A Mutation：G102A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.01 Å |
| 9B2T Haspin bound to nucleosome in position 2 Deposited 2024-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G102A Mutation：G102A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.99 Å |
| 9B2U Haspin bound to H3 tail Deposited 2024-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
1–136（136 aa）
|
Mutation：G102A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.64 Å |
| 9CA7 Cryo-EM structure of human SRCAP-nucleosome complex in the fully-engaged state (composite structure) Deposited 2024-06-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric |
Chain U
2–136（135 aa）
Chain W
2–136（135 aa）
|
Not recorded | AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 5 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 9CA8 Cryo-EM structure of human SRCAP-nucleosome complex in the partially-engaged state (composite structure) Deposited 2024-06-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric |
Chain U
2–136（135 aa）
Chain W
2–136（135 aa）
|
Not recorded | AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 5 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.92 Å |
| 9CAA Cryo-EM structure of human SRCAP-nucleosome complex in the pre-engaged state (composite structure) Deposited 2024-06-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric |
Chain U
2–136（135 aa）
Chain W
2–136（135 aa）
|
Not recorded | AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.04 Å |
| 9CAB Cryo-EM structure of human SRCAP-nucleosome complex in the encounter state (composite structure) Deposited 2024-06-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric |
Chain U
2–136（135 aa）
Chain W
2–136（135 aa）
|
Not recorded | AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 5 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.94 Å |
| 9CG9 Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2 Deposited 2024-06-28 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：G102A, C110A Mutation：G102A, C110A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；3 uL of sample was applied to grid.
|
Resolution 2.94 Å |
| 9DBY ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome Deposited 2024-08-24 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G103A Mutation：G103A | ZN ZINC ION × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9DDE ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome Deposited 2024-08-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G103A Mutation：G103A | ZN ZINC ION × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9DG3 ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome Deposited 2024-09-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G103A Mutation：G103A | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.46 Å |
| 9DGG ncPRC1RYBP bound to unmodified nucleosome Deposited 2024-09-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：G103A Mutation：G103A | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 9E1L Snf2h bound nucleosome complex - ClassA1 Deposited 2024-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.15 Å |
| 9E1M Snf2h bound nucleosome complex - ClassA2 Deposited 2024-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 9E1N Snf2h bound nucleosome complex-ClassA3 Deposited 2024-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9E1O Snf2h bound nucleosome complex - ClassB1 Deposited 2024-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9E1P Snf2h bound nucleosome complex - ClassB2 Deposited 2024-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 9E1Q Snf2h bound nucleosome complex - ClassB3 Deposited 2024-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9E1R Snf2h bound nucleosome complex - ClassB4 Deposited 2024-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9E1U Snf2h bound nucleosome complex - ClassC1 Deposited 2024-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9E1V Snf2h bound nucleosome complex - ClassC2 Deposited 2024-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9E1W Snf2h bound nucleosome complex - ClassC3 Deposited 2024-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9E1X Snf2h bound nucleosome complex - ClassD1 Deposited 2024-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9E1Y Empty Nucleosome with 601 widom sequence Deposited 2024-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 9EIL SIRT6 bound to an H3K27Ac nucleosome Deposited 2024-11-26 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ZSL [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3aR,5R,6R,6aR)-6-hydroxytetrahydro-2H-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9F0O The molecular basis and modulation of lamin-specific chromatin interaction Deposited 2024-04-17 | Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
39–136（98 aa）
Chain E
39–136（98 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 9GD0 Structure of a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9GD1 Structure of Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 9GD2 Structure of Chd1 bound to a dinucleosome with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 9GD3 Structure of a mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA. Deposited 2024-08-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9GEN Recombinant Myeloperoxidase bound to nucleosome core particle Deposited 2024-08-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
38–136（99 aa）
Chain E
38–136（99 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.76 Å |
| 9GEO Nucleosome core particle Deposited 2024-08-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
38–136（99 aa）
Chain E
38–136（99 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.79 Å |
| 9GEP Native monomeric Myeloperoxidase bound to nucleosome core particle Deposited 2024-08-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric |
Chain A
38–136（99 aa）
Chain E
38–136（99 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.89 Å |
| 9GEQ Native dimeric Myeloperoxidase bound to nucleosome core particle; composite map Deposited 2024-08-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain A
38–136（99 aa）
Chain E
38–136（99 aa）
|
Not recorded | CL CHLORIDE ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.12 Å |
| 9GER Native dimeric Myeloperoxidase bound to nucleosome core particle, intermediate state; composite map Deposited 2024-08-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain A
38–136（99 aa）
Chain E
38–136（99 aa）
|
Not recorded | CL CHLORIDE ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.58 Å |
| 9IHD Nucleosome core particle bound by one molecule of DTT-reduced native monomeric myeloperoxidase Deposited 2025-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric |
Chain A
38–136（99 aa）
Chain E
38–136（99 aa）
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.97 Å |
| 9IHE Nucleosome core particle bound by two molecules of DTT-reduced native monomeric myeloperoxidase Deposited 2025-02-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain A
38–136（99 aa）
Chain E
38–136（99 aa）
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.95 Å |
| 9IHF Nucleosome core particle bound by one monomer and one dimer of of DTT-reduced native myeloperoxidase Deposited 2025-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric |
Chain A
38–136（99 aa）
Chain E
38–136（99 aa）
|
Not recorded | HEM PROTOPORPHYRIN IX CONTAINING FE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 9N6K 2.88 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex with DNA-binding domain Deposited 2025-02-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
40–136（97 aa）
Chain E
40–136（97 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9NH8 CHD1-nucleosome complex (anchored state) Deposited 2025-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain V
1–136（136 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ARG ARGININE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9NY4 USP21 bound to H2AK119ub nucleosome Deposited 2025-03-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 9QAJ Structure of the nucleosome-bound human BCL7A Deposited 2025-02-28 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.95 Å |
| 9R5K Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20mM Hepes, 120mM Nacl
cryo-EM vitrification conditions
Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity
|
Resolution 4.20 Å |
| 9R5S Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20mM Hepes, 120mM Nacl
cryo-EM vitrification conditions
Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity
|
Resolution 3.80 Å |
| 9R5W Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20mM Hepes, 120mM Nacl
cryo-EM vitrification conditions
Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity
|
Resolution 3.80 Å |
| 9SI3 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome Deposited 2025-08-28 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.83 Å |
| 9SI9 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class0) Deposited 2025-08-28 | Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain A
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.86 Å |
| 9SJ5 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class1) Deposited 2025-08-29 | Different mutation/modification Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.85 Å |
| 9SLJ Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Double Occupancy) Deposited 2025-09-04 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 9T4V ALC1/CHD1L in an intermediate conformation, bound to a PARylated nucleosome Deposited 2025-11-02 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；3 uL were applied on grid and immediately blotted for 2.5 s at blot force 0.
|
Resolution 6.60 Å |
| 9W74 Cryo-EM structure of the close-packed di-hexasome (CPDH) Deposited 2025-08-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.94 Å |
| 9WBZ The structure of NCP-motor-ARP module of ncBAF-nucleosome complex Deposited 2025-08-15 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain E
2–136（135 aa）
Chain K
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9WC0 The structure of NCP-RA module of ncBAF-nucleosome complex Deposited 2025-08-15 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain E
2–136（135 aa）
Chain K
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å |
| 9XYC Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome LEDGF+nucleosome map Q Deposited 2025-08-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9Y4P Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker Deposited 2025-09-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric |
Chain E
2–136（135 aa）
Chain Q
2–136（135 aa）
Chain W
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.84 Å |
230 other PDB entries and 239 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | H32_XENLA |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–135； UniProt 2–136 Author chain E； PDBConstruct 1–135； UniProt 2–136 |
