Histone H3.1
Homo sapiens
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 × 14 DNA 2 PDB declaration: hexadecameric（16） Consistent with all polymer counts | Chain A； UniProt 1–136 Chain E； UniProt 1–136 Chain K； UniProt 1–136 Chain O； UniProt 1–136 | Not recorded | Histone H4 × 4 （P62805） Histone H2A type 1-B/E × 3 （P04908） Histone H2B type 1-J × 3 （P06899） DNA (250-MER) × 1 DNA (250-MER) × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；potassium bromide, potassium thiocyanate, Tris-HCl, PGA-LM, PEG 400 | Resolution 3.14 Å R-free 0.255 |
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 5GSE | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2B2T Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 and phosphothreonine 3 Deposited 2005-09-19 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
1–19（19 aa）
Fragment：residues 1-19
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；283 K；4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00
|
Resolution 2.45 Å R-free 0.266 |
| 2B2U Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 and dimethylarginine 2 Deposited 2005-09-19 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
1–15（15 aa）
Fragment：residues 1-15
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；283 K；4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00
|
Resolution 2.95 Å R-free 0.290 |
| 2B2V Crystal structure analysis of human CHD1 chromodomains 1 and 2 bound to histone H3 resi 1-15 MeK4 Deposited 2005-09-19 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
1–15（15 aa）
Fragment：residues 1-15
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；283 K；4% PEG3350, 0.05M HEPES, pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00
|
Resolution 2.65 Å R-free 0.266 |
| 2B2W Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 Deposited 2005-09-19 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
1–19（19 aa）
Fragment：residues 1-19
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；283 K；4% PEG3350, 0.05M HEPES pH 8.0, 10mM BTP, 12.5mM NaCl, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00
|
Resolution 2.40 Å R-free 0.273 |
| 2CV5 Crystal structure of human nucleosome core particle Deposited 2005-05-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
0–135（136 aa）
Chain E
0–135（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 9 CL CHLORIDE ION × 4 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.50 Å R-free 0.277 |
| 2L75 Solution structure of CHD4-PHD2 in complex with H3K9me3 Deposited 2010-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–14（13 aa）
Fragment：UNP residues 2-14
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 15；Pressure ambient
NMR sample composition
1 mM CHD4-PHD2-1; 1 mM H3K9me3-2, 20 uM DSS-3; 1 mM DTT-4; 5 mM sodium chloride-5; 10 mM sodium phosphate-6; 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
1 mM [U-100% 13C; U-100% 15N] CHD4-PHD2-7; 1.1 mM H3K9me3-8; 20 uM DSS-9; 1 mM DTT-10; 5 mM sodium chloride-11; 10 mM sodium phosphate-12; 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition
1 mM [U-100% 13C; U-100% 15N] CHD4-PHD2-13; 1.1 mM H3K9me3-14; 20 uM DSS-15; 1 mM DTT-16; 5 mM sodium chloride-17; 10 mM sodium phosphate-18; 100% D2O | 100% D2O
|
Resolution not provided |
| 2RI7 Crystal structure of PHD finger-linker-bromodomain Y17E mutant from human BPTF in the H3(1-9)K4ME2 bound state Deposited 2007-10-10 | 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 P
2–10（9 aa）
Fragment：N-terminal tail residues 2-10
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 GOL GLYCEROL × 1 IPA ISOPROPYL ALCOHOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；BPTF Y17E PHD finger-linker-bromodomain (16.5 mg/ml, 20 mM Tris-HCl pH 7.5, 50 mM KCl) was pre-incubated with three-fold molar excess of H3(1-9)K4me2 peptide in the presence of 5 mM MgCl2 for about 30 min on ice. Drops were made by mixing 2 l each of the complex with the reservoir solution: 8.5% isopropanol, 0.085 M Hepes-Na, pH 7.5, 17% PEG 4000, 15% Glycerol. A 0.3 l of 1 M KCl was then added to the drops as additive., VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.45 Å R-free 0.192 |
| 2UXN Structural Basis of Histone Demethylation by LSD1 Revealed by Suicide Inactivation Deposited 2007-03-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
2–22（21 aa）
Fragment：HISTONE H3-DERIVED SUICIDE INHIBITOR, RESIDUES 2-22
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FDA DIHYDROFLAVINE-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.6；PROTEIN: 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, AND 5 MM DTT RESERVOIR: 0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, AND 10 MM DTT
|
Resolution 2.72 Å R-free 0.272 |
| 3A1B Crystal structure of the DNMT3A ADD domain in complex with histone H3 Deposited 2009-03-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–21（20 aa）
Fragment：ADD(ATRX-DNMT3-DNMT3L) domain(residues 476-614), UNP residues 2-21(Histone H3.1)
|
Not recorded | ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；10% PEG 2000 monomethyl ether, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.29 Å R-free 0.224 |
| 3AFA The human nucleosome structure Deposited 2010-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.50 Å R-free 0.270 |
| 3AYW Crystal Structure of Human Nucleosome Core Particle Containing H3K56Q mutation Deposited 2011-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K56Q Mutation：K56Q | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.90 Å R-free 0.273 |
| 3AZE Crystal Structure of Human Nucleosome Core Particle Containing H3K64Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K64Q Mutation：K64Q | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.00 Å R-free 0.302 |
| 3AZF Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K79Q Mutation：K79Q | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.70 Å R-free 0.263 |
| 3AZG Crystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K115Q Mutation：K115Q | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.40 Å R-free 0.269 |
| 3AZH Crystal Structure of Human Nucleosome Core Particle Containing H3K122Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K122Q Mutation：K122Q | CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.49 Å R-free 0.266 |
| 3AZI Crystal Structure of Human Nucleosome Core Particle Containing H4K31Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.70 Å R-free 0.289 |
| 3AZJ Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.89 Å R-free 0.268 |
| 3AZK Crystal Structure of Human Nucleosome Core Particle Containing H4K59Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.20 Å R-free 0.258 |
| 3AZL Crystal Structure of Human Nucleosome Core Particle Containing H4K77Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.70 Å R-free 0.259 |
| 3AZM Crystal Structure of Human Nucleosome Core Particle Containing H4K79Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.89 Å R-free 0.296 |
| 3AZN Crystal Structure of Human Nucleosome Core Particle Containing H4K91Q mutation Deposited 2011-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.00 Å R-free 0.254 |
| 3KMT Crystal structure of vSET/SAH/H3 ternary complex Deposited 2009-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
26–33（8 aa）
Fragment：residues 26-33
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.78 Å R-free 0.224 |
| 3KMT Crystal structure of vSET/SAH/H3 ternary complex Deposited 2009-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
26–33（8 aa）
Fragment：residues 26-33
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.78 Å R-free 0.224 |
| 3KMT Crystal structure of vSET/SAH/H3 ternary complex Deposited 2009-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain I
26–33（8 aa）
Fragment：residues 26-33
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.78 Å R-free 0.224 |
| 3KMT Crystal structure of vSET/SAH/H3 ternary complex Deposited 2009-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain G
26–33（8 aa）
Fragment：residues 26-33
Chain H
26–33（8 aa）
Fragment：residues 26-33
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.78 Å R-free 0.224 |
| 3KMT Crystal structure of vSET/SAH/H3 ternary complex Deposited 2009-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain I
26–33（8 aa）
Fragment：residues 26-33
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；26% PEG 4000, 0.1 M sodium citrate pH 6.3, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.78 Å R-free 0.224 |
| 3KQI crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide Deposited 2009-11-17 | 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 B
1–12（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；2.0 M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.78 Å R-free 0.218 |
| 3KQI crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide Deposited 2009-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–12（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 4 GOL GLYCEROL × 2 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；2.0 M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.78 Å R-free 0.218 |
| 3LQI Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide Deposited 2010-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain R
2–10（9 aa）
Fragment：Histone H3 N-terminal tail
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；293 K；0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.92 Å R-free 0.241 |
| 3LQI Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide Deposited 2010-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain S
2–10（9 aa）
Fragment：Histone H3 N-terminal tail
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；293 K；0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.92 Å R-free 0.241 |
| 3LQI Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide Deposited 2010-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain T
2–10（9 aa）
Fragment：Histone H3 N-terminal tail
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；293 K；0.1 M Bis-Tris, 0.2 M ammonium acetate, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.92 Å R-free 0.241 |
| 3LQJ Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me3 peptide Deposited 2010-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Q
2–10（9 aa）
Fragment：Histone H3 N-terminal tail
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；293 K；0.1 M Tris, 0.2 M Li2SO4, 15% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.274 |
| 3LQJ Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me3 peptide Deposited 2010-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain T
2–10（9 aa）
Fragment：Histone H3 N-terminal tail
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；293 K；0.1 M Tris, 0.2 M Li2SO4, 15% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.274 |
| 3O34 Crystal structure of TRIM24 PHD-Bromo complexed with H3(13-32)K23ac peptide Deposited 2010-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
14–33（20 aa）
Fragment：UNP residues 14-35
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 BTN BIOTIN × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；100 mM Na-citrate (pH 5.6), 200 mM K/Na-tartrate tetrahydrate and 1.6 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.241 |
| 3O35 Crystal structure of TRIM24 PHD-Bromo complexed with H3(23-31)K27ac peptide Deposited 2010-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
24–32（9 aa）
Fragment：UNP residues 14 -22
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；200 mM Na-acetate, 30% Polyethylene glycol 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.76 Å R-free 0.225 |
| 3O35 Crystal structure of TRIM24 PHD-Bromo complexed with H3(23-31)K27ac peptide Deposited 2010-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
24–32（9 aa）
Fragment：UNP residues 14 -22
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；200 mM Na-acetate, 30% Polyethylene glycol 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.76 Å R-free 0.225 |
| 3O37 Crystal structure of TRIM24 PHD-Bromo complexed with H3(1-10)K4 peptide Deposited 2010-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM Tris (pH 7.5), 30% Polyethylene glycol monomethyl ether 5000 and 100 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.254 |
| 3O37 Crystal structure of TRIM24 PHD-Bromo complexed with H3(1-10)K4 peptide Deposited 2010-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM Tris (pH 7.5), 30% Polyethylene glycol monomethyl ether 5000 and 100 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.254 |
| 3O37 Crystal structure of TRIM24 PHD-Bromo complexed with H3(1-10)K4 peptide Deposited 2010-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM Tris (pH 7.5), 30% Polyethylene glycol monomethyl ether 5000 and 100 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.254 |
| 3O37 Crystal structure of TRIM24 PHD-Bromo complexed with H3(1-10)K4 peptide Deposited 2010-07-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；50 mM Tris (pH 7.5), 30% Polyethylene glycol monomethyl ether 5000 and 100 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.254 |
| 3U4S Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine Deposited 2011-10-10 | 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 C
8–15（8 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 08P N-(carboxycarbonyl)-D-cysteine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG 3350, 0.1M citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.15 Å R-free 0.222 |
| 3U4S Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine Deposited 2011-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
8–15（8 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 08P N-(carboxycarbonyl)-D-cysteine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG 3350, 0.1M citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.15 Å R-free 0.222 |
| 3U5N Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-20)K9me3K14ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–21（20 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9 and acetylated K14, UNP residues 2-21
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M ammonium tartrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.95 Å R-free 0.256 |
| 3U5N Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-20)K9me3K14ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–21（20 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9 and acetylated K14, UNP residues 2-21
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M ammonium tartrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.95 Å R-free 0.256 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain I
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain J
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain K
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain L
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain M
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain N
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain O
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5O Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-22)K9me3K14acK18ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
2–23（22 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14 and K18, UNP residues 2-23
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M sodium citrate and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.280 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain I
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain J
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain K
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain L
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain M
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain N
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain O
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3U5P Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide Deposited 2011-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
2–29（28 aa）
Fragment：N-terminal histone H3 peptide containing trimethylated K9, acetylated K14, K18 and K23, UNP residues 2-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M lithium sulfate, 0.1 mM Tris pH 8.0 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.265 |
| 3V43 Crystal structure of MOZ Deposited 2011-12-14 | 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 Q
2–19（18 aa）
Fragment：UNP RESIDUES 2-19
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 4 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.2M ammonium acetate, 0.1M tri-sodium citrate, 30% w/v PEG 4000, pH 5.6, vapor diffusion, hanging drop, temperature 293K
|
Resolution 1.47 Å R-free 0.176 |
| 3W96 Crystal Structure of Human Nucleosome Core Particle lacking H2A N-terminal region Deposited 2013-04-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 1 MN MANGANESE (II) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.00 Å R-free 0.296 |
| 3W97 Crystal Structure of Human Nucleosome Core Particle lacking H2B N-terminal region Deposited 2013-04-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.20 Å R-free 0.321 |
| 3W98 Crystal Structure of Human Nucleosome Core Particle lacking H3.1 N-terminal region Deposited 2013-04-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
29–136（108 aa）
Fragment：UNP residues 29-136
Chain E
29–136（108 aa）
Fragment：UNP residues 29-136
|
Not recorded | MN MANGANESE (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.42 Å R-free 0.303 |
| 3W99 Crystal Structure of Human Nucleosome Core Particle lacking H4 N-terminal region Deposited 2013-04-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；POTASSIUM CACODYLATE, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 3.00 Å R-free 0.312 |
| 3WA9 The nucleosome containing human H2A.Z.1 Deposited 2013-04-30 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.07 Å R-free 0.271 |
| 3WAA The nucleosome containing human H2A.Z.2 Deposited 2013-04-30 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.20 Å R-free 0.271 |
| 3WKJ The nucleosome containing human TSH2B Deposited 2013-10-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.291 |
| 3X1S Crystal structure of the nucleosome core particle Deposited 2014-11-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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；298 K；60-70mM KCL, 70-90mM MnCl2, 24% MPD, 20mM Na-Cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.81 Å R-free 0.270 |
| 3X1T Crystal structure of nucleosome core particle consisting of mouse testis specific histone variants H2aa and H2ba Deposited 2014-11-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 22 CL CHLORIDE ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70mM Kcl, 70-90mM MnCl2, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.81 Å R-free 0.266 |
| 3X1U Crystal structure of nucleosome core particle in the presence of histone variants involved in reprogramming Deposited 2014-11-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 4 CL CHLORIDE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70 mM KCl, 70-90 mM MnCl2, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.25 Å R-free 0.270 |
| 3X1V Crystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming Deposited 2014-11-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 19 CL CHLORIDE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；60-70 mM KCl, 70-90 mM MnCl2, Na-cocodylate, 24% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.92 Å R-free 0.259 |
| 3ZVY PHD finger of human UHRF1 in complex with unmodified histone H3 N- terminal tail Deposited 2011-07-28 | 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 D
2–9（8 aa）
Fragment：RESIDUES 2-9
|
Not recorded | ZN ZINC ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；290 K；CRYSTALS WERE OBTAINED AT 17 DEGREES USING THE VAPOR DIFFUSION METHOD BY MIXING A PROTEIN SOLUTION AT A CONCENTRATION OF 606 MICROM (IN 20 MM TRIS PH 7, 150 MM NACL, 0.5 MM TCEP, 25 MICROM ZNCL2 AND 0.1 MM PMSF) AND 10-FOLD EXCESS OF PEPTIDE WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (0.1 M TRIS PH 8.5, 0.2 M MGCL2, 30 % PEG 4000). CRYSTALS WERE CRYOPROTECTED WITH 15 % MPD AND FLASH FROZEN IN LIQUID NITROGEN.
|
Resolution 1.95 Å R-free 0.227 |
| 3ZVY PHD finger of human UHRF1 in complex with unmodified histone H3 N- terminal tail Deposited 2011-07-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–9（8 aa）
Fragment：RESIDUES 2-9
|
Not recorded | ZN ZINC ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；290 K；CRYSTALS WERE OBTAINED AT 17 DEGREES USING THE VAPOR DIFFUSION METHOD BY MIXING A PROTEIN SOLUTION AT A CONCENTRATION OF 606 MICROM (IN 20 MM TRIS PH 7, 150 MM NACL, 0.5 MM TCEP, 25 MICROM ZNCL2 AND 0.1 MM PMSF) AND 10-FOLD EXCESS OF PEPTIDE WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION (0.1 M TRIS PH 8.5, 0.2 M MGCL2, 30 % PEG 4000). CRYSTALS WERE CRYOPROTECTED WITH 15 % MPD AND FLASH FROZEN IN LIQUID NITROGEN.
|
Resolution 1.95 Å R-free 0.227 |
| 4BD3 Phf19 links methylated lysine 36 of histone H3 to regulation of Polycomb activity Deposited 2012-10-04 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
32–42（11 aa）
Fragment：H3(31-41)K36ME3, RESIDUES 32-42
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure 1.0
NMR sample composition
90% WATER/10% D2O
|
Resolution not provided |
| 4C1Q Crystal structure of the PRDM9 SET domain in complex with H3K4me2 and AdoHcy. Deposited 2013-08-13 | 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 C
2–11（10 aa）
Fragment：N-TERMINUS, RESIDUES 2-11
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.5；278 K；0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 5.5 AND 25% W/V PEG3350
|
Resolution 2.30 Å R-free 0.252 |
| 4F4U The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5 Deposited 2012-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
5–16（12 aa）
Fragment：UNP residue 5-16
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；16% PEG 4000, 6% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.261 |
| 4F4U The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5 Deposited 2012-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
5–16（12 aa）
Fragment：UNP residue 5-16
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；16% PEG 4000, 6% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.261 |
| 4F56 The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5 Deposited 2012-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
5–16（12 aa）
Fragment：UNP residue 5-16
|
Not recorded | ZN ZINC ION × 1 CGK 3-[(2R,3aR,5R,6R,6aR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-2,6-dihydroxytetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]propanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% PEG 10000, 0.1M Tris, pH 8.5, vapor diffusion, hanging drop, temperature 298K
|
Resolution 1.70 Å R-free 0.233 |
| 4F56 The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5 Deposited 2012-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
5–16（12 aa）
Fragment：UNP residue 5-16
|
Not recorded | ZN ZINC ION × 1 CGK 3-[(2R,3aR,5R,6R,6aR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-2,6-dihydroxytetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]propanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% PEG 10000, 0.1M Tris, pH 8.5, vapor diffusion, hanging drop, temperature 298K
|
Resolution 1.70 Å R-free 0.233 |
| 4FT2 crystal structure of Zea mays ZMET2 in complex H3(1-15)K9me2 peptide and SAH Deposited 2012-06-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain P
16–30（15 aa）
Fragment：histone H3 peptide, UNP residues 16-30
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.2 M calcium acetate, 0.1 M imidazole pH 8.0, and 10% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.20 Å R-free 0.277 |
| 4FT4 crystal structure of Zea mays ZMET2 in complex H3(1-32)K9me2 peptide and SAH Deposited 2012-06-27 | 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 Q
33–64（32 aa）
Fragment：histone H3 peptide, UNP residues 33-64
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M sodium citrate, 0.1 M bis-tris propane, pH 6.5 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.70 Å R-free 0.248 |
| 4FT4 crystal structure of Zea mays ZMET2 in complex H3(1-32)K9me2 peptide and SAH Deposited 2012-06-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain P
33–64（32 aa）
Fragment：histone H3 peptide, UNP residues 33-64
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M sodium citrate, 0.1 M bis-tris propane, pH 6.5 and 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.70 Å R-free 0.248 |
| 4FWF Complex structure of LSD2/AOF1/KDM1b with H3K4 mimic Deposited 2012-07-01 | 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
2–21（20 aa）
Fragment：UNP residues 2-21
|
Mutation：K4M | ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；298 K；21% PEG3350, 200mM diammonium citrate, pH 7, VAPOR DIFFUSION, temperature 298K
|
Resolution 2.70 Å R-free 0.237 |
| 4LK9 Crystal Structure of MOZ double PHD finger histone H3 tail complex Deposited 2013-07-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–22（21 aa）
Fragment：unp residues 2-22
|
Not recorded | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；283 K；100 mM Na-Hepes, 1.4 M sodium citrate, pH 7.5, VAPOR DIFFUSION, temperature 283K
|
Resolution 1.60 Å R-free 0.186 |
| 4LKA Crystal Structure of MOZ double PHD finger histone H3K9ac complex Deposited 2013-07-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–22（21 aa）
Fragment：unp residues 2-22
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；283 K；100 mM Na-Hepes, 1.4 M sodium citrate, pH 7.5, vapor diffusion, temperature 283K
|
Resolution 1.61 Å R-free 0.185 |
| 4LLB Crystal Structure of MOZ double PHD finger histone H3K14ac complex Deposited 2013-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–22（21 aa）
Fragment：unp residues 2-22
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；283 K；100 mM Tris-Cl, 200 mM Li2SO4, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, temperature 283K
|
Resolution 2.50 Å R-free 0.266 |
| 4LLB Crystal Structure of MOZ double PHD finger histone H3K14ac complex Deposited 2013-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–22（21 aa）
Fragment：unp residues 2-22
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；283 K；100 mM Tris-Cl, 200 mM Li2SO4, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, temperature 283K
|
Resolution 2.50 Å R-free 0.266 |
| 4N4H Crystal structure of the Bromo-PWWP of the mouse zinc finger MYND-type containing 11 isoform alpha in complex with histone H3.1K36me3 Deposited 2013-10-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
22–43（22 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.3；289 K；25% (w/v) polyethylene glycol 4000, 0.1M Tris-HCl, pH 8.3, 0.2M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.30 Å R-free 0.263 |
| 4UP0 Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and a H3K4me2 peptide Deposited 2014-06-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
2–16（15 aa）
Fragment：RESIDUES 2-16
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
1 M SODIUM CITRATE, 0.1 M TRIS PH 7, 0.2 M NACL
|
Resolution 1.28 Å R-free 0.166 |
| 4YM5 Crystal structure of the human nucleosome containing 6-4PP (inside) Deposited 2015-03-06 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 4.00 Å R-free 0.289 |
| 4YM6 Crystal structure of the human nucleosome containing 6-4PP (outside) Deposited 2015-03-06 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 3.51 Å R-free 0.287 |
| 4Z0R Crystal Structure of the CW domain of ZCWPW2 mutant F78R in complex with histone H3 peptide Deposited 2015-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–16（15 aa）
Fragment：N-terminal tail (UNP residues 2-16)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 UNX UNKNOWN LIGAND × 9 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；2 M ammonium sulfate, 2% PEG400, 0.1 M HEPES sodium
|
Resolution 1.75 Å R-free 0.192 |
| 4Z2M Crystal structure of human SPT16 Mid-AID/H3-H4 tetramer FACT Histone complex Deposited 2015-03-30 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain G
35–136（102 aa）
Fragment：UNP residues 35-136
Chain I
35–136（102 aa）
Fragment：UNP residues 35-136
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；10% PEG400, 0.9-1.1 M Imidazole, 100-150 mM L-histidine
|
Resolution 2.98 Å R-free 0.246 |
| 5AV5 human nucleosome core particle Deposited 2015-06-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
LIQUID DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 2.40 Å R-free 0.233 |
| 5AV6 human nucleosome core particle Deposited 2015-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 2.20 Å R-free 0.229 |
| 5AV8 human nucleosome core particle Deposited 2015-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 2.20 Å R-free 0.233 |
| 5AV9 human nucleosome core particle Deposited 2015-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 2.20 Å R-free 0.239 |
| 5AVB human nucleosome core particle Deposited 2015-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 2.40 Å R-free 0.236 |
| 5AVC human nucleosome core particle Deposited 2015-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 2.40 Å R-free 0.238 |
| 5B24 The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer Deposited 2015-12-31 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 3.60 Å R-free 0.249 |
| 5B2I Human nucleosome containing CpG unmethylated DNA Deposited 2016-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 3.00 Å R-free 0.257 |
| 5B2J Human nucleosome containing CpG methylated DNA Deposited 2016-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, manganese(II) chloride, potassium chloride
|
Resolution 2.60 Å R-free 0.252 |
| 5B31 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.1. Deposited 2016-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.20 Å R-free 0.271 |
| 5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain J
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
|
Resolution 3.50 Å R-free 0.253 |
| 5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
|
Resolution 3.50 Å R-free 0.253 |
| 5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
|
Resolution 3.50 Å R-free 0.253 |
| 5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain N
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
|
Resolution 3.50 Å R-free 0.253 |
| 5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain R
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
|
Resolution 3.50 Å R-free 0.253 |
| 5C3I Crystal structure of the quaternary complex of histone H3-H4 heterodimer with chaperone ASF1 and the replicative helicase subunit MCM2 Deposited 2015-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain V
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；20% PEG 3350, 2% Tacsimate,0.1 M Tris-HCl pH 8.0
|
Resolution 3.50 Å R-free 0.253 |
| 5CPI Nucleosome containing unmethylated Sat2R DNA Deposited 2015-07-21 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.90 Å R-free 0.295 |
| 5CPJ Nucleosome containing methylated Sat2R DNA Deposited 2015-07-21 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 3.15 Å R-free 0.295 |
| 5CPK Nucleosome containing methylated Sat2L DNA Deposited 2015-07-21 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.63 Å R-free 0.284 |
| 5GSU Crystal structure of nucleosome core particle consisting of human testis-specific histone variants, Th2A and Th2B Deposited 2016-08-17 | 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
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | CL CHLORIDE ION × 3 MN MANGANESE (II) ION × 15 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；20mM Pottasium Cacodylate pH 6.0, 60-70mM KCl, 70-90mM MnCl2
|
Resolution 3.10 Å R-free 0.257 |
| 5GT0 Crystal structure of nucleosome complex with human testis-specific histone variants, Th2a Deposited 2016-08-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 14 CL CHLORIDE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；60-70mM KCl, 70-90mM MnCl2, 24% MPD
|
Resolution 2.82 Å R-free 0.280 |
| 5GT3 Crystal structure of nucleosome particle in the presence of human testis-specific histone variant, hTh2b Deposited 2016-08-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 12 CL CHLORIDE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；60-70mM KCl, 70-90mM MnCl2, 24% MPD
|
Resolution 2.91 Å R-free 0.258 |
| 5GTC Crystal structure of complex between DMAP-SH conjugated with a Kaposi's sarcoma herpesvirus LANA peptide (5-15) and nucleosome core particle Deposited 2016-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.70 Å R-free 0.267 |
| 5HJB AF9 YEATS in complex with histone H3 Crotonylation at K9 Deposited 2016-01-12 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
4–11（8 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；20% (w/v) polyethylene glycol 4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 3% MPD
|
Resolution 2.70 Å R-free 0.253 |
| 5HJC BRD3 second bromodomain in complex with histone H3 acetylation at K18 Deposited 2016-01-13 | 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 B
16–24（9 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30%(w/v) polyethylene glycol methyl ether 5000, 0.2 M ammonium sulfate, 0.1 M MES, 0.1 M guanidine hydrochloride
|
Resolution 2.60 Å R-free 0.269 |
| 5HJD AF9 YEATS in complex with histone H3 Crotonylation at K18 Deposited 2016-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain B
15–21（7 aa）
Chain D
15–21（7 aa）
Chain F
15–21（7 aa）
Chain L
15–21（7 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) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 3 SO4 SULFATE ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；20%(w/v) polyethylene glycol 4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.1 M copper chloride dihydrate
|
Resolution 2.81 Å R-free 0.273 |
| 5HJD AF9 YEATS in complex with histone H3 Crotonylation at K18 Deposited 2016-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain H
15–21（7 aa）
Chain I
15–21（7 aa）
Chain J
15–21（7 aa）
Chain M
15–21（7 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) Non-standard monomer：Yes (specific site not provided by mmCIF) | CU COPPER (II) ION × 1 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；20%(w/v) polyethylene glycol 4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.1 M copper chloride dihydrate
|
Resolution 2.81 Å R-free 0.273 |
| 5IQL Crystal structure of YEATS2 YEATS bound to H3K27cr peptide Deposited 2016-03-11 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
25–32（8 aa）
Fragment：H3 peptide (UNP RESIDUES 25-32)
|
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；pH 7；291 K；0.1M Bis-Tris propane, 4.0 M NH4Ac, pH 7.0
|
Resolution 2.10 Å R-free 0.253 |
| 5J9S ENL YEATS in complex with histone H3 acetylation at K27 Deposited 2016-04-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
16–40（25 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1M K/Na Tartrate, 0.1M Sodium citrate tribasic dihydrate, pH 5.6, 2M (NH4)2SO4
|
Resolution 2.70 Å R-free 0.210 |
| 5JRG Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF) Deposited 2016-05-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 15 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.50 Å R-free 0.245 |
| 5KKL Structure of ctPRC2 in complex with H3K27me3 and H3K27M Deposited 2016-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
23–31（9 aa）
|
Mutation：K2027M | ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；15% PEG4000, 175mM ammonium citrate, pH 7.0
|
Resolution 2.94 Å R-free 0.234 |
| 5T1G chromo shadow domain of CBX1 in complex with a histone peptide Deposited 2016-08-19 | 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 B
39–53（15 aa）
Fragment：unp residues 39-53
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.5 M sodium citrate, 0.1 M HEPES
|
Resolution 1.90 Å R-free 0.243 |
| 5T1I CBX3 chromo shadow domain in complex with histone H3 peptide Deposited 2016-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
39–53（15 aa）
Fragment：unp residues 39-53
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG 3350, 0.2 M sodium chloride, 0.1 M Hepes, 5% Ethylene Glycol
|
Resolution 1.60 Å R-free 0.239 |
| 5T8R Crystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer Deposited 2016-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 2 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2.2 M Na/K phosphate
|
Resolution 2.40 Å R-free 0.235 |
| 5T8R Crystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer Deposited 2016-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2.2 M Na/K phosphate
|
Resolution 2.40 Å R-free 0.235 |
| 5T8R Crystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer Deposited 2016-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 4 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2.2 M Na/K phosphate
|
Resolution 2.40 Å R-free 0.235 |
| 5T8R Crystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer Deposited 2016-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
2–11（10 aa）
Fragment：UNP residues 2-11
|
Not recorded | ZN ZINC ION × 4 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；2.2 M Na/K phosphate
|
Resolution 2.40 Å R-free 0.235 |
| 5TBN Solution NMR structure of PHF20 PHD domain in complex with a histone H3K4me2 peptide Deposited 2016-09-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–12（11 aa）
Fragment：residues 2-12
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate；Pressure 101325
NMR sample composition
1.5 mM [U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1.5 mM [U-13C; U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
2 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 5VA6 CRYSTAL STRUCTURE OF ATXR5 IN COMPLEX WITH HISTONE H3.1 MONO-METHYLATED ON R26 Deposited 2017-03-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
20–37（18 aa）
Fragment：residues 20-37
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；50% polypropylene glycol 400, 5% DMSO, 0.1 M HEPES-NaOH (pH 6.0)
|
Resolution 2.40 Å R-free 0.297 |
| 5VA6 CRYSTAL STRUCTURE OF ATXR5 IN COMPLEX WITH HISTONE H3.1 MONO-METHYLATED ON R26 Deposited 2017-03-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
20–37（18 aa）
Fragment：residues 20-37
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；50% polypropylene glycol 400, 5% DMSO, 0.1 M HEPES-NaOH (pH 6.0)
|
Resolution 2.40 Å R-free 0.297 |
| 5WFC Humanized mutant of the Chaetomium thermophilum Polycomb Repressive Complex 2 bound to the inhibitor GSK343 Deposited 2017-07-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
23–33（11 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 8 A97 N-[(6-methyl-2-oxo-4-propyl-1,2-dihydropyridin-3-yl)methyl]-6-[2-(4-methylpiperazin-1-yl)pyridin-4-yl]-1-(propan-2-yl)-1H-indazole-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM sodium malonate pH 7.0, 16% PEG 3350, 43 mM 3-cyclohexyl-1-propylphosphocholine
|
Resolution 2.28 Å R-free 0.203 |
| 5WVO Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3 Deposited 2016-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
2–37（36 aa）
Fragment：UNP residues 2-37
|
Mutation：K18C,K23C | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；100mM Bis-Tris (pH 6.0), 200mM lithium sulfate monohydrate, 20% PEG 10000
|
Resolution 2.00 Å R-free 0.239 |
| 5XF3 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,R-configuration) Deposited 2017-04-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RRK (1R,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
|
Resolution 2.60 Å R-free 0.270 |
| 5XF4 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (S,S-configuration) Deposited 2017-04-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 SSK (1S,2S)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；35-55 mM MnCl2, 25-49 mM KCl, 20 mM K-Cacodylate pH 6.0
|
Resolution 2.87 Å R-free 0.266 |
| 5XF5 Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,S-configuration) Deposited 2017-04-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MG MAGNESIUM ION × 1 RUD [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 × 2 RSK (1S,2R)-1,2-diphenylethane-1,2-diamine × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；35-55mM MnCl2, 25-49mM KCl, 20mM K-Cacodylate pH 6.0
|
Resolution 2.82 Å R-free 0.264 |
| 5XFR Ternary complex of MTF2, DNA and histone Deposited 2017-04-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric |
Chain C
34–41（8 aa）
Chain D
34–41（8 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M MES monohydrate-pH 6.5, 0.2M ammonium sulfate, 25% PEG monomethyl ether 5000, 10% glycerol
|
Resolution 2.25 Å R-free 0.231 |
| 5Y0C Crystal Structure of the human nucleosome at 2.09 angstrom resolution Deposited 2017-07-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 10 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.09 Å R-free 0.249 |
| 5Y0D Crystal Structure of the human nucleosome containing the H2B E76K mutant Deposited 2017-07-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 1.99 Å R-free 0.252 |
| 5Z23 Crystal structure of the nucleosome containing a chimeric histone H3/CENP-A CATD Deposited 2017-12-28 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–75（75 aa）
Chain A
114–136（23 aa）
Chain E
1–75（75 aa）
Chain E
114–136（23 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.73 Å R-free 0.261 |
| 5Z30 The crystal structure of the nucleosome containing a cancer-associated histone H2A.Z R80C mutant Deposited 2018-01-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.45 Å R-free 0.243 |
| 5ZBX The crystal structure of the nucleosome containing histone H3.1 CATD(V76Q, K77D) Deposited 2018-02-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–75（75 aa）
Chain A
114–136（23 aa）
Chain E
1–75（75 aa）
Chain E
114–136（23 aa）
|
Mutation：V76Q, K77D Mutation：V76Q, K77D Mutation：V76Q, K77D Mutation：V76Q, K77D | CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.58 Å R-free 0.249 |
| 6BHD Crystal structure of SETDB1 with a modified H3 peptide Deposited 2017-10-30 | 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 B
5–20（16 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 35 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% glycerol
|
Resolution 1.25 Å R-free 0.183 |
| 6BHE Crystal structure of SETDB1 with a modified H3 peptide Deposited 2017-10-30 | 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 B
5–20（16 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 36 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% glycerol
|
Resolution 1.35 Å R-free 0.172 |
| 6BHG Crystal structure of SETDB1 with a modified H3 peptide Deposited 2017-10-30 | 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 B
5–20（16 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 40 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；291 K；20% PEG5000 MME, 0.1 M Bis-Tris
|
Resolution 1.45 Å R-free 0.176 |
| 6BHH Crystal structure of SETDB1 with a modified H3 peptide Deposited 2017-10-30 | 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 B
5–20（16 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 UNX UNKNOWN LIGAND × 26 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；25% PEG3350, 0.2 M lithium sulfate, 0.1 M HEPES
|
Resolution 1.85 Å R-free 0.237 |
| 6BHI Crystal structure of SETDB1 with a modified H3 peptide Deposited 2017-10-30 | 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 B
5–20（16 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 35 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；25% PEG3350, 0.2 M lithium sulfate, 0.1 M HEPES
|
Resolution 1.40 Å R-free 0.187 |
| 6D07 Crystal structure of the complex between human chromobox homolog 1 (CBX1) and H3K9me3 peptide Deposited 2018-04-10 | 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 C
2–16（15 aa）
Fragment：H3K9(me)3 peptide (UNP residues 2-16)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M sodium chloride, 0.1 M Tris, pH 8.0, 30% w/v PEG3350
|
Resolution 2.10 Å R-free 0.257 |
| 6D07 Crystal structure of the complex between human chromobox homolog 1 (CBX1) and H3K9me3 peptide Deposited 2018-04-10 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–16（15 aa）
Fragment：H3K9(me)3 peptide (UNP residues 2-16)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M sodium chloride, 0.1 M Tris, pH 8.0, 30% w/v PEG3350
|
Resolution 2.10 Å R-free 0.257 |
| 6D08 Crystal structure of an engineered bump-hole complex of mutant human chromobox homolog 1 (CBX1) with H3K9bn peptide Deposited 2018-04-10 | 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 C
2–16（15 aa）
Fragment：H3K9bn peptide (UNP residues 2-16)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 2 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M citrate, pH 5.0, 3 M ammonium sulfate
|
Resolution 2.10 Å R-free 0.252 |
| 6D08 Crystal structure of an engineered bump-hole complex of mutant human chromobox homolog 1 (CBX1) with H3K9bn peptide Deposited 2018-04-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–16（15 aa）
Fragment：H3K9bn peptide (UNP residues 2-16)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 2 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M citrate, pH 5.0, 3 M ammonium sulfate
|
Resolution 2.10 Å R-free 0.252 |
| 6HKT Structure of an H1-bound 6-nucleosome array Deposited 2018-09-08 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 48 PDB declaration: 50-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）
Chain U
1–136（136 aa）
Chain Y
1–136（136 aa）
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
Chain k
1–136（136 aa）
Chain o
1–136（136 aa）
Chain u
1–136（136 aa）
Chain y
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.8；293.15 K；15% MPD, 0.1 M NaCl and 0.1 M Tris pH 8.8
|
Resolution 9.70 Å R-free 0.286 |
| 6HTS Cryo-EM structure of the human INO80 complex bound to nucleosome Deposited 2018-10-04 | 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 × 17 PDB declaration: nonadecameric |
Chain I
1–136（136 aa）
Chain M
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 6IPU Human nucleosome core particle containing 145 bp of DNA Deposited 2018-11-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
39–136（98 aa）
Chain E
39–136（98 aa）
|
Not recorded | CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
|
Resolution 1.99 Å R-free 0.263 |
| 6IQ4 Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups. Deposited 2018-11-06 | 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
39–136（98 aa）
Chain E
39–136（98 aa）
|
Not recorded | AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 4 D0X [Ru(eta(6)-p-cymene)Cl-2(pta) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
|
Resolution 2.25 Å R-free 0.257 |
| 6JOU Crystal structure of the human nucleosome containing H2A.Z.1 S42R Deposited 2019-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.17 Å R-free 0.250 |
| 6JR0 Crystal structure of the human nucleosome phased with 12 selenium atoms Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
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) | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.50 Å R-free 0.253 |
| 6JR1 Crystal structure of the human nucleosome phased with 16 selenium atoms Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
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) | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.40 Å R-free 0.243 |
| 6JXD Human nucleosome core particle with cohesive end DNA termini Deposited 2019-04-23 | 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
39–136（98 aa）
Chain E
39–135（97 aa）
|
Not recorded | MN MANGANESE (II) ION × 17 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；manganese chloride, potassium chloride, potassium cacodylate
|
Resolution 2.25 Å R-free 0.292 |
| 6K1I Human nucleosome core particle with gammaH2A.X variant Deposited 2019-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 23 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；potassium chloride, manganese chloride, potassium cacodylate
|
Resolution 2.75 Å R-free 0.277 |
| 6K1J Human nucleosome core particle with H2A.X variant Deposited 2019-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Potassium Chloride, Manganese Chloride, Potassium Cacodylate
|
Resolution 2.85 Å R-free 0.319 |
| 6K1K Human nucleosome core particle with H2A.X S139E variant Deposited 2019-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 33 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；potassium chloride, manganese chloride, potassium cacodylate
|
Resolution 2.20 Å R-free 0.275 |
| 6KE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
41–136（96 aa）
Chain E
41–136（96 aa）
|
Not recorded | MN MANGANESE (II) ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
|
Resolution 2.22 Å R-free 0.230 |
| 6KVD Crystal structure of human nucleosome containing H2A.J Deposited 2019-09-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MN MANGANESE (II) ION × 13 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.21 Å R-free 0.257 |
| 6L49 H3-CA-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric |
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
Chain S
1–136（136 aa）
Chain W
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 18.90 Å |
| 6L4A H3-H3-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-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）
Chain S
1–136（136 aa）
Chain W
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 12.30 Å |
| 6L9H The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
41–136（96 aa）
Chain E
41–136（96 aa）
|
Not recorded | MN MANGANESE (II) ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
|
Resolution 2.60 Å R-free 0.278 |
| 6L9Z 338 bp di-nucleosome assembled with linker histone H1.X Deposited 2019-11-11 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric |
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 | CL CHLORIDE ION × 8 CA CALCIUM ION × 65 K POTASSIUM ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate
|
Resolution 2.50 Å R-free 0.256 |
| 6LA2 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-11 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 38-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）
Chain U
1–136（136 aa）
Chain Y
1–136（136 aa）
Chain e
1–136（136 aa）
Chain i
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, Potassium chloride, Sodium acetate
|
Resolution 3.89 Å R-free 0.267 |
| 6LA8 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 Deposited 2019-11-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric |
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 | CA CALCIUM ION × 23 K POTASSIUM ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate (cryo-25% MPD)
|
Resolution 3.40 Å R-free 0.265 |
| 6LA9 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0 (high cryoprotectant) Deposited 2019-11-12 | Different oligomeric state Different ligand/ion 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）
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | CA CALCIUM ION × 40 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
|
Resolution 3.70 Å R-free 0.266 |
| 6LAB 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0 Deposited 2019-11-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-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 | CA CALCIUM ION × 20 K POTASSIUM ION × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
|
Resolution 3.20 Å R-free 0.262 |
| 6LE9 The Human Telomeric Nucleosome Displays Distinct Structural and Dynamic Properties Deposited 2019-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
41–136（96 aa）
Chain E
41–136（96 aa）
|
Not recorded | MN MANGANESE (II) ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；Manganase chloride, potassium chloride, potassium cacodylate, MPD and trehalose
|
Resolution 2.60 Å R-free 0.281 |
| 6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CA CALCIUM ION × 6 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
|
Resolution 3.00 Å R-free 0.261 |
| 6LER 169 bp nucleosome harboring non-identical cohesive DNA termini. Deposited 2019-11-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 | CA CALCIUM ION × 8 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；Calcium chloride, potassium chloride, sodium acetate
|
Resolution 3.00 Å R-free 0.261 |
| 6M3V 355 bp di-nucleosome harboring cohesive DNA termini Deposited 2020-03-04 | 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
1–136（136 aa）
Chain E
1–136（136 aa）
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | K POTASSIUM ION × 1 CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
|
Resolution 4.60 Å R-free 0.261 |
| 6M44 355 bp di-nucleosome harboring cohesive DNA termini (high cryoprotectant) Deposited 2020-03-05 | 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
1–136（136 aa）
Chain E
1–136（136 aa）
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | CA CALCIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Calcium chloride, Potassium chloride, Potassium Cacodylate, Poly glutamic acid
|
Resolution 3.81 Å R-free 0.286 |
| 6M4D Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-06 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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 4.40 Å |
| 6M4G Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-06 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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 2.80 Å |
| 6M4H Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-07 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 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 3.90 Å |
| 6R8Y Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
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 4.30 Å |
| 6R8Z Cryo-EM structure of NCP_THF2(-1)-UV-DDB Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
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 3.90 Å |
| 6R90 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
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 4.50 Å |
| 6R91 Cryo-EM structure of NCP_THF2(-3)-UV-DDB Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
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 4.10 Å |
| 6R92 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
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 4.80 Å |
| 6R93 Cryo-EM structure of NCP-6-4PP Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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 4.00 Å |
| 6R94 Cryo-EM structure of NCP_THF2(-3) Deposited 2019-04-02 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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 |
| 6T90 OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2019-10-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–134（134 aa）
|
Not recorded | PTD PENTANEDIAL × 9 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.05 Å |
| 6T93 Nucleosome with OCT4-SOX2 motif at SHL-6 Deposited 2019-10-25 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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 3.49 Å |
| 6UPK Structure of FACT_subnucleosome complex 1 Deposited 2019-10-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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 4.90 Å |
| 6UPL Structure of FACT_subnucleosome complex 2 Deposited 2019-10-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
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 7.40 Å |
| 6USJ Structure of two nucleosomes bridged by human PARP2 Deposited 2019-10-27 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-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 7.5；Buffer was pH-adjusted and filtered through a 0.22 um filter.
cryo-EM vitrification conditions
Cryogen ETHANE；Blot time 2s, blot force 0
|
Resolution 10.50 Å |
| 6V2K The nucleosome structure after H2A-H2B exchange Deposited 2019-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.60 Å R-free 0.248 |
| 6V41 crystal structure of CDY1 chromodomain bound to H3K9me3 Deposited 2019-11-27 | 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 QQQ
2–16（15 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 20 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；1.4 M sodium citrate, 0.1 M HEPES
|
Resolution 1.60 Å R-free 0.215 |
| 6V92 RSC-NCP Deposited 2019-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 33 PDB declaration: 35-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 20.00 Å |
| 6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
32–43（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 17 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
|
Resolution 1.70 Å R-free 0.241 |
| 6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
32–43（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
|
Resolution 1.70 Å R-free 0.241 |
| 6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
32–43（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
|
Resolution 1.70 Å R-free 0.241 |
| 6WAV Crystal structure of PHF1 in complex with H3K36me3 substitution Deposited 2020-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
32–43（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UNX UNKNOWN LIGAND × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6
|
Resolution 1.70 Å R-free 0.241 |
| 6WW4 Crystal structure of HERC2 ZZ domain in complex with histone H3 tail Deposited 2020-05-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–7（6 aa）
Fragment：fusion protein
|
Not recorded | ZN ZINC ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 17% PEG 10000
|
Resolution 2.25 Å R-free 0.243 |
| 6WW4 Crystal structure of HERC2 ZZ domain in complex with histone H3 tail Deposited 2020-05-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–7（6 aa）
Fragment：fusion protein
|
Not recorded | ZN ZINC ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, and 17% PEG 10000
|
Resolution 2.25 Å R-free 0.243 |
| 6YIH Structure of Chromosomal Passenger Complex (CPC) bound to phosphorylated Histone 3 peptide at 2.6 A. Deposited 2020-04-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain D
2–13（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；291 K；20 % (w/v) PEG 4,000, 100 mM HEPES pH 7.0, 150 mM ammonium sulphate
|
Resolution 2.55 Å R-free 0.259 |
| 6YOV OCT4-SOX2-bound nucleosome - SHL+6 Deposited 2020-04-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–134（134 aa）
|
Not recorded | PTD PENTANEDIAL × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 7BWD Structure of Dot1L-H2BK34ub Nucleosome Complex Deposited 2020-04-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 4.32 Å |
| 7C0M Human cGAS-nucleosome complex Deposited 2020-05-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-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 | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7CCQ Structure of the 1:1 cGAS-nucleosome complex Deposited 2020-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
39–136（98 aa）
Chain E
39–136（98 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7CCR Structure of the 2:2 cGAS-nucleosome complex Deposited 2020-06-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric |
Chain A
39–136（98 aa）
Chain E
39–136（98 aa）
Chain L
39–136（98 aa）
Chain P
39–136（98 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.90 Å |
| 7COW 353 bp di-nucleosome harboring cohesive DNA termini with linker histone H1.0 Deposited 2020-08-05 | Different oligomeric state Different ligand/ion 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）
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | CA CALCIUM ION × 3 K POTASSIUM ION × 5 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291.15 K；potassium acetate, calcium chloride, potassium chloride
|
Resolution 2.86 Å R-free 0.297 |
| 7D1Z Cryo-EM structure of SET8-nucleosome complex Deposited 2020-09-15 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.15 Å |
| 7DBP Linker histone defines structure and self-association behaviour of the 177 bp human chromosome Deposited 2020-10-21 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 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 ETHANE
|
Resolution 4.50 Å |
| 7E8D NSD2 E1099K mutant bound to nucleosome Deposited 2021-03-01 | 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 × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 3 SFG SINEFUNGIN × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7K5X Cryo-EM structure of a chromatosome containing human linker histone H1.0 Deposited 2020-09-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
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 2.93 Å |
| 7K5Y Cryo-EM structure of a chromatosome containing human linker histone H1.4 Deposited 2020-09-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
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 2.76 Å |
| 7K60 Cryo-EM structure of a chromatosome containing human linker histone H1.10 Deposited 2020-09-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
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 3.12 Å |
| 7K61 Cryo-EM structure of 197bp nucleosome aided by scFv Deposited 2020-09-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
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 2.85 Å |
| 7K63 Cryo-EM structure of a chromatosome containing chimeric linker histone gH1.10-ncH1.4 Deposited 2020-09-18 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
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 3.03 Å |
| 7KLR Solution structure of the PHD1 domain of histone demethylase KDM5A in complex with a histone H3(1-10) peptide Deposited 2020-10-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–11（10 aa）
|
Not recorded | ZN ZINC ION × 2 |
SOLUTION NMR
NMR measurement conditions
pH 7.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition
900 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 4000 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
550 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 800 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
1250 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 400 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 7LBK Crystal structure of human Survivin bound to histone H3 T3phK4me3 peptide Deposited 2021-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
2–13（12 aa）
Chain D
2–13（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；The crystal was obtained by mixing 1 uL of protein at 10 mg/mL with 1 uL of mother liquor composed of 0.16 M potassium/sodium tartrate, 14% PEG 3350.
|
Resolution 2.70 Å R-free 0.253 |
| 7LBO Crystal structure of human Survivin bound to histone H3 T3phK4me1 peptide Deposited 2021-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
2–13（12 aa）
Chain F
2–13（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；1 uL of protein at 10 mg/mL was mixed with 1 uL of buffer composed of 0.16 M potassium/sodium tartrate, 12% PEG 3350
|
Resolution 2.50 Å R-free 0.261 |
| 7LBP Crystal structure of human Survivin bound to histone H3T3phK4ac peptide Deposited 2021-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
2–13（12 aa）
Chain D
2–13（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；1 uL of protein at 10mg/mL was mixed with 1 uL of buffer composed of 0.16 M potassium/sodium tartrate, 12% PEG 3350
|
Resolution 2.60 Å R-free 0.247 |
| 7LBQ Crystal structure of human Survivin bound to histone H3 T3phK4me2 peptide Deposited 2021-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
2–13（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；1 uL of protein was mixed with 1uL of buffer composed of 2.25 mM spermine, 9 mM MgCl2, 0.9 mM spermidine, 1.8 mM cobalt (III)hexamine chloride, 0.05 sodium cacodylate pH 7.0, 5% PEG 400
|
Resolution 2.69 Å R-free 0.268 |
| 7LYA Cryo-EM structure of the human nucleosome core particle with linked histone proteins H2A and H2B Deposited 2021-03-06 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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 2.91 Å |
| 7LYB Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Deposited 2021-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.28 Å |
| 7LYC Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777) Deposited 2021-03-06 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
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 2.94 Å |
| 7MJU Crystal structure of human AF10 PZP bound to histone H3 tail Deposited 2021-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–14（13 aa）
|
Not recorded | ZN ZINC ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.09 M Tris, 22.5% PEG 3350, and 10 mM spermine tetrahydrochloride
|
Resolution 2.10 Å R-free 0.206 |
| 7NL0 Cryo-EM structure of the Lin28B nucleosome core particle Deposited 2021-02-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7SCY Nuc147 bound to single BRCT Deposited 2021-09-29 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
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 4.10 Å |
| 7SCZ Nuc147 bound to multiple BRCTs Deposited 2021-09-29 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
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 3.50 Å |
| 7U0G structure of LIN28b nucleosome bound 3 OCT4 Deposited 2022-02-18 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 13 PDB declaration: pentadecameric |
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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 7U0I Structure of LIN28b nucleosome bound 2 OCT4 Deposited 2022-02-18 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information 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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 7U0J Structure of 162bp LIN28b nucleosome Deposited 2022-02-18 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 7V6Q Crystal structure of sNASP-ASF1A-H3.1-H4 complex Deposited 2021-08-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–136（136 aa）
|
Not recorded | GOL GLYCEROL × 4 1PE PENTAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；18% (v/v) Tacsimate, pH 5.0
11% (v/v) PEG2000MME
|
Resolution 3.00 Å R-free 0.203 |
| 7V6Q Crystal structure of sNASP-ASF1A-H3.1-H4 complex Deposited 2021-08-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
1–136（136 aa）
|
Not recorded | GOL GLYCEROL × 2 1PE PENTAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；18% (v/v) Tacsimate, pH 5.0
11% (v/v) PEG2000MME
|
Resolution 3.00 Å R-free 0.203 |
| 7V90 Telomeric mononucleosome Deposited 2021-08-24 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7V96 Telomeric Dinucleosome Deposited 2021-08-24 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric |
Chain A
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 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.92 Å |
| 7V9C Telomeric Dinucleosome in open state Deposited 2021-08-24 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric |
Chain A
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 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 7V9J Telomeric trinucleosome Deposited 2021-08-25 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-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）
Chain S
1–136（136 aa）
Chain W
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.00 Å |
| 7V9K Telomeric tetranucleosome Deposited 2021-08-25 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-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）
Chain S
1–136（136 aa）
Chain W
1–136（136 aa）
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 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.10 Å |
| 7V9S Telomeric trinucleosome in open state Deposited 2021-08-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-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）
Chain S
1–136（136 aa）
Chain W
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 11.00 Å |
| 7VA4 Telomeric tetranucleosome in open state Deposited 2021-08-27 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-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）
Chain S
1–136（136 aa）
Chain W
1–136（136 aa）
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 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 14.00 Å |
| 7VZ4 Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA sequence Deposited 2021-11-15 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 1.89 Å |
| 7W9V Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) Deposited 2021-12-10 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.95 Å |
| 7X57 Cryo-EM structure of human subnucleosome (closed form) Deposited 2022-03-04 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain C
2–136（135 aa）
Chain E
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 3.63 Å |
| 7X58 Cryo-EM structure of human subnucleosome (open form) Deposited 2022-03-04 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain C
2–136（135 aa）
Chain E
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 3.93 Å |
| 7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain U
1–136（136 aa）
Chain Y
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
|
Resolution 3.51 Å R-free 0.280 |
| 7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric |
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
Chain e
1–136（136 aa）
Chain i
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
|
Resolution 3.51 Å R-free 0.280 |
| 7XVM Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-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 | CA CALCIUM ION × 18 CL CHLORIDE ION × 3 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
|
Resolution 2.84 Å R-free 0.259 |
| 7XX5 Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 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 | CA CALCIUM ION × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
|
Resolution 3.19 Å R-free 0.259 |
| 7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 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 | CA CALCIUM ION × 21 K POTASSIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
|
Resolution 3.39 Å R-free 0.296 |
| 7XX6 Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-28 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric |
Chain U
1–136（136 aa）
Chain Y
1–136（136 aa）
Chain e
1–136（136 aa）
Chain i
1–136（136 aa）
|
Not recorded | CA CALCIUM ION × 26 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
|
Resolution 3.39 Å R-free 0.296 |
| 7XZX Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain Deposited 2022-06-03 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
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 4.53 Å |
| 7XZY Cryo-EM structure of the nucleosome containing 193 base-pair DNA with a p53 target sequence Deposited 2022-06-03 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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 3.97 Å |
| 7XZZ Cryo-EM structure of the nucleosome in complex with p53 Deposited 2022-06-03 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
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 4.07 Å |
| 7Y00 Cryo-EM structure of the nucleosome containing 169 base-pair DNA with a p53 target sequence Deposited 2022-06-03 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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 3.96 Å |
| 7Y5U Cryo-EM structure of the monomeric human CAF1LC-H3-H4 complex Deposited 2022-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain D
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7Y5V Cryo-EM structure of the dimeric human CAF1LC-H3-H4 complex Deposited 2022-06-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain D
1–136（136 aa）
Chain I
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.10 Å |
| 7Y5W Cryo-EM structure of the left-handed Di-tetrasome Deposited 2022-06-17 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain C
1–136（136 aa）
Chain E
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7Y60 Cryo-EM structure of human CAF1LC bound right-handed Di-tetrasome Deposited 2022-06-18 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain C
1–136（136 aa）
Chain E
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7Y61 Cryo-EM structure of the two CAF1LCs bound right-handed Di-tetrasome Deposited 2022-06-18 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–136（136 aa）
Chain C
1–136（136 aa）
Chain E
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.60 Å |
| 7Y7I chicken KNL2 in complex with the CENP-A nucleosome Deposited 2022-06-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–64（64 aa）
Chain E
1–64（64 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 7YOZ Cryo-EM structure of human subnucleosome (intermediate form) Deposited 2022-08-02 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain C
2–136（135 aa）
Chain E
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 4.30 Å |
| 7YQK cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1 Deposited 2022-08-07 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
37–136（100 aa）
Chain E
37–136（100 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.38 Å |
| 7ZI4 Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Deposited 2022-04-07 | 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 × 18 PDB declaration: eicosameric |
Chain I
1–136（136 aa）
Chain M
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；4uL of sample applied to Quantifoil R2/2 Cu 300 mesh grids. blot parameters were wait time 30 sec, blot time 0.5 sec, blot force -8
|
Resolution 3.20 Å |
| 8DK5 Structure of 187bp LIN28b nucleosome with site 0 mutation Deposited 2022-07-02 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.71 Å |
| 8EVG 162bp CX3CR1 nucleosome (further classified with better nucleosome end) Deposited 2022-10-20 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.75 Å |
| 8EVH CX3CR1 nucleosome and wild type PU.1 complex Deposited 2022-10-20 | Different construct Different mutation/modification Different oligomeric state Different experimental method 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）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.85 Å |
| 8EVI CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations Deposited 2022-10-20 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.64 Å |
| 8EVJ CX3CR1 nucleosome bound PU.1 and C/EBPa Deposited 2022-10-20 | Different construct Different mutation/modification Different oligomeric state Different experimental method 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）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.1
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8GE0 Crystal structure of JADE1 PZP domain in complex with Histone H3 Deposited 2023-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–14（13 aa）
|
Not recorded | ZN ZINC ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000
|
Resolution 2.40 Å R-free 0.241 |
| 8GE0 Crystal structure of JADE1 PZP domain in complex with Histone H3 Deposited 2023-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–14（13 aa）
|
Not recorded | ZN ZINC ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000
|
Resolution 2.40 Å R-free 0.241 |
| 8GE0 Crystal structure of JADE1 PZP domain in complex with Histone H3 Deposited 2023-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
2–14（13 aa）
|
Not recorded | ZN ZINC ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000
|
Resolution 2.40 Å R-free 0.241 |
| 8GUI Bre1-nucleosome complex (Model I) Deposited 2022-09-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.81 Å |
| 8GUJ Bre1-nucleosome complex (Model II) Deposited 2022-09-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8GUK Human nucleosome core particle (free form) Deposited 2022-09-12 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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 2.51 Å |
| 8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric |
Chain a
2–136（135 aa）
Chain e
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric |
Chain a
2–136（135 aa）
Chain e
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 8H1T Cryo-EM structure of BAP1-ASXL1 bound to chromatosome Deposited 2022-10-04 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 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 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8HAG Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (3.2 angstrom resolution) Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8HAH Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (3.9 angstrom resolution) Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8HAI Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (4.7 angstrom resolution) Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.70 Å |
| 8HAJ Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 2 (4.8 angstrom resolution) Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 8HAK Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (4.5 angstrom resolution) Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 8HAL Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 1 Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 8HAM Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 2 Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 8HAN Cryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 3 Deposited 2022-10-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 8IEG Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deposited 2023-02-15 | 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 × 11 PDB declaration: tridecameric |
Chain E
38–135（98 aa）
Chain K
38–135（98 aa）
|
Not recorded | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.44 Å |
| 8IEJ RNF20-RNF40/hRad6A-Ub/nucleosome complex Deposited 2023-02-15 | 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 × 11 PDB declaration: tridecameric |
Chain E
38–135（98 aa）
Chain K
38–135（98 aa）
|
Not recorded | ZN ZINC ION × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.12 Å |
| 8IHL Overlapping tri-nucleosome Deposited 2023-02-23 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
Chain K
2–136（135 aa）
Chain M
2–136（135 aa）
Chain Q
2–136（135 aa）
Chain U
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 7.64 Å |
| 8IIY Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K14ac peptide Deposited 2023-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
2–20（19 aa）
Chain C
2–20（19 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris buffer (pH 8.5) containing 20% (w/v) PEG monomethyl ether 2000, 200 mM trimethylamine N-oxide
|
Resolution 2.15 Å R-free 0.247 |
| 8IIZ Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K27ac peptide Deposited 2023-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
2–33（32 aa）
Chain C
2–33（32 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Tris buffer (pH 8.5) containing 20% (w/v) PEG monomethyl ether 2000, 200 mM trimethylamine N-oxide
|
Resolution 2.10 Å R-free 0.301 |
| 8IJ0 Crystal structure of GAS41 YEATS domain in complex with H3K9ac peptide Deposited 2023-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2–12（11 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 3 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Na-HEPES buffer (pH 7.5) containing 5% (w/v) PEG 400 and 2 M ammonium sulfate
|
Resolution 1.52 Å R-free 0.189 |
| 8IJ0 Crystal structure of GAS41 YEATS domain in complex with H3K9ac peptide Deposited 2023-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2–12（11 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 3 SO4 SULFATE ION × 4 1PE PENTAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Na-HEPES buffer (pH 7.5) containing 5% (w/v) PEG 400 and 2 M ammonium sulfate
|
Resolution 1.52 Å R-free 0.189 |
| 8IQF Cryo-EM structure of the dimeric human CAF1-H3-H4 complex Deposited 2023-03-16 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain D
1–136（136 aa）
Chain I
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 8IQG Cryo-EM structure of the monomeric human CAF1-H3-H4 complex Deposited 2023-03-16 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain D
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8J6S Cryo-EM structure of the single CAF-1 bound right-handed Di-tetrasome Deposited 2023-04-26 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain C
1–136（136 aa）
Chain E
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8J6T Cryo-EM structure of the double CAF-1 bound right-handed Di-tetrasome Deposited 2023-04-26 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–136（136 aa）
Chain C
1–136（136 aa）
Chain E
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Hepes, pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.60 Å |
| 8JBX Human canonical 601 DNA nucleosome Deposited 2023-05-09 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 8JCC Human histone H2B variant H2BFWT Cryo-EM structure with 601 DNA sequence Deposited 2023-05-10 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 8JCD Human H2BFWTH100R nucleosome with 601 DNA Deposited 2023-05-11 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.14 Å |
| 8JHF Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–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 SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
|
Resolution 3.68 Å |
| 8JHG Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–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 SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane
|
Resolution 3.58 Å |
| 8JL9 Cryo-EM structure of the human nucleosome with scFv Deposited 2023-06-02 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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 2.65 Å |
| 8JLA Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 Deposited 2023-06-02 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
29–136（108 aa）
Chain E
29–136（108 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.44 Å |
| 8JND The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-06-06 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 19-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 3.66 Å |
| 8JNE The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding Deposited 2023-06-06 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-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 4.68 Å |
| 8JNF The cryo-EM structure of the RAD51 filament bound to the nucleosome Deposited 2023-06-06 | Different construct Different mutation/modification Different experimental method 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）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.91 Å |
| 8KCY Structure of nucleosome complexed with two DEK molecules Deposited 2023-08-08 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 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 2.80 Å |
| 8KD1 Structure of nucleosome complexed with one DEK molecule Deposited 2023-08-08 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 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
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8KE0 Structure of H1.2 bound to the nucleosome Deposited 2023-08-11 | Different construct Different mutation/modification Different oligomeric state Different experimental method 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
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8OFF Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes (Map1) Deposited 2023-03-15 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric |
Chain Ca
1–135（135 aa）
Chain Cb
1–135（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；blot force = 0 N
blot time = 8 s
|
Resolution 3.40 Å |
| 8OO7 CryoEM Structure INO80core Hexasome complex composite model state1 Deposited 2023-04-04 | 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 × 16 PDB declaration: 18-meric |
Chain M
2–136（135 aa）
Chain Q
2–136（135 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 7 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；30mM HEPES, pH7.5
50mM NaCl
0.25mM CaCl2
0.25mM DTT
2mM ADP
3.3mM MgCl2
10mM NaF
2mM AlCl3
0.05% octyl-beta-glucoside
cryo-EM vitrification conditions
Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
|
Resolution 2.80 Å |
| 8OOA CryoEM Structure INO80core Hexasome complex Hexasome refinement state1 Deposited 2023-04-04 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric |
Chain M
2–136（135 aa）
Chain Q
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；30mM HEPES, pH7.5
50mM NaCl
0.25mM CaCl2
0.25mM DTT
2mM ADP
3.3mM MgCl2
10mM NaF
2mM AlCl3
0.05% octyl-beta-glucoside
cryo-EM vitrification conditions
Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
|
Resolution 3.18 Å |
| 8OOP CryoEM Structure INO80core Hexasome complex composite model state2 Deposited 2023-04-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric |
Chain M
2–136（135 aa）
Chain Q
2–136（135 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 2 ALF TETRAFLUOROALUMINATE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；30mM HEPES, pH7.5
50mM NaCl
0.25mM CaCl2
0.25mM DTT
2mM ADP
3.3mM MgCl2
10mM NaF
2mM AlCl3
0.05% octyl-beta-glucoside
cryo-EM vitrification conditions
Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
|
Resolution 2.70 Å |
| 8OOS CryoEM Structure INO80core Hexasome complex ATPase-hexasome refinement state 2 Deposited 2023-04-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain M
2–136（135 aa）
Chain Q
2–136（135 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ALF TETRAFLUOROALUMINATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；30mM HEPES, pH7.5
50mM NaCl
0.25mM CaCl2
0.25mM DTT
2mM ADP
3.3mM MgCl2
10mM NaF
2mM AlCl3
0.05% octyl-beta-glucoside
cryo-EM vitrification conditions
Cryogen ETHANE；wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807)
|
Resolution 3.29 Å |
| 8OSJ Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Deposited 2023-04-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
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 6.20 Å |
| 8OSK Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) Deposited 2023-04-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8OSL Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement) Deposited 2023-04-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.90 Å |
| 8OTS OCT4 and MYC-MAX co-bound to a nucleosome Deposited 2023-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | PTD PENTANEDIAL × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8OTT MYC-MAX bound to a nucleosome at SHL+5.8 Deposited 2023-04-21 | 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 × 10 PDB declaration: dodecameric |
Chain A
40–134（95 aa）
Chain E
40–134（95 aa）
|
Not recorded | PTD PENTANEDIAL × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8OX0 Structure of apo telomeric nucleosome Deposited 2023-04-28 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；25 mM HEPES-KOH pH 8.0, 150 mM KCl, 1 mM MgCl2, 1% glycerol, 0.01% Igepal CA-630,1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；Blot Force: -15
Blot Time: 2.5 s
|
Resolution 2.52 Å |
| 8OX1 Structure of TRF1core in complex with telomeric nucleosome Deposited 2023-04-28 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；25 mM HEPES-KOH pH 8.0, 150 mM KCl, 1 mM MgCl2, 1% glycerol, 0.01% Igepal CA-630,
1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；Blot Force: -15
Blot Time: 2.5 s
|
Resolution 2.70 Å |
| 8Q36 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound) Deposited 2023-08-03 | 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 AAA
39–136（98 aa）
Chain EEE
39–136（98 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0].
|
Resolution 2.60 Å R-free 0.262 |
| 8Q3E High Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide Deposited 2023-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain AAA
39–136（98 aa）
Chain EEE
39–136（98 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
|
Resolution 2.17 Å R-free 0.270 |
| 8Q3M Structure of Nucleosome Core with a Bound Kaposi Sarcoma Associated Herpesvirus LANA Peptide Having a Methionine to Ornithine Substitution Deposited 2023-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain AAA
39–136（98 aa）
Chain EEE
39–136（98 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
|
Resolution 2.50 Å R-free 0.268 |
| 8Q3X Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Kaposi Sarcoma Associated Herpesvirus LANA Peptide-Au[I] Compound) Deposited 2023-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain AAA
39–136（98 aa）
Chain EEE
39–136（98 aa）
|
Not recorded | AU GOLD ION × 1 XIS 4-diphenylphosphanylbenzoic acid × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]
|
Resolution 2.30 Å R-free 0.262 |
| 8QKT Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment Deposited 2023-09-17 | 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 AAA
39–136（98 aa）
Chain EEE
39–136（98 aa）
|
Not recorded | MN MANGANESE (II) ION × 19 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；MnCl2-containing buffers
|
Resolution 3.26 Å R-free 0.321 |
| 8QKT Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment Deposited 2023-09-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain KKK
39–136（98 aa）
Chain OOO
39–136（98 aa）
|
Not recorded | MN MANGANESE (II) ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；MnCl2-containing buffers
|
Resolution 3.26 Å R-free 0.321 |
| 8RGM Cryo-EM structure of nucleosome containing Widom603 DNA Deposited 2023-12-14 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8SMW Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 1) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8SMX Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 2) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8SMY Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8SMZ Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8SN0 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 5) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8SN1 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 6) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8SN2 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c (UbcH5c chemically conjugated to histone H2A) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8SN3 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8SN4 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8SN6 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 4) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN7 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN8 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 6) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8SN9 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 1) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8SNA Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c with backside ubiquitin (UbcH5c chemically conjugated to histone H2A) (class 2) Deposited 2023-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8SPS High resolution structure of ESRRB nucleosome bound OCT4 at site a and site b Deposited 2023-05-03 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information 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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8SPU Structure of ESRRB nucleosome bound OCT4 at site c Deposited 2023-05-03 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric |
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 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8SWI Crystal structure of legAS4 from Legionella pneumophila subsp. pneumophila with histone H3 (1-12)peptide Deposited 2023-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–13（12 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M Bis-Tris 6.5 and 38% PPG P400
|
Resolution 3.00 Å R-free 0.310 |
| 8SYP Genomic CX3CR1 nucleosome Deposited 2023-05-25 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 8TXV Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 1) Deposited 2023-08-24 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
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 3.80 Å |
| 8TXW Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 2) Deposited 2023-08-24 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
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 3.60 Å |
| 8TXX Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A K15 in complex with RNF168 (Class 3) Deposited 2023-08-24 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
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 3.70 Å |
| 8U13 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 1) Deposited 2023-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8U14 Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A lysine 15 in complex with RNF168-UbcH5c (class 2) Deposited 2023-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8U9S Cryo-EM structure of NRCAM nucleosome aided by scFv Deposited 2023-09-20 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
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 |
| 8UBJ Cryo-EM structure of NRCAM nucleosome aided by scFv (3D Flex map) Deposited 2023-09-23 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
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 2.80 Å |
| 8UBK Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome Deposited 2023-09-23 | Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
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 |
| 8UBL Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome (3D Flex map) Deposited 2023-09-23 | Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
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 2.80 Å |
| 8UPF Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Deposited 2023-10-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8VFX Cryo-EM structure of 186bp ALBN1 nucleosome aided by scFv Deposited 2023-12-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
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 2.65 Å |
| 8VFY Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1) Deposited 2023-12-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 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 ETHANE
|
Resolution 2.89 Å |
| 8VFZ Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2) Deposited 2023-12-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
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 4.10 Å |
| 8VG0 Cryo-EM structure of GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 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 3.07 Å |
| 8VG1 Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric |
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 2.48 Å |
| 8VG2 Cryo-EM structure of FoxA1 and GATA4 in complex with H14 chromatosome Deposited 2023-12-22 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
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 3.04 Å |
| 8VLR Cryo-EM structure of native H2AK119bu nucleosome at 2.6 Deposited 2024-01-12 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
39–136（98 aa）
Chain E
39–136（98 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM Tris-HCl, pH 7.5, 50 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 8VMI PRC2_AJ119-450 bound to H3K4me3 Deposited 2024-01-13 | 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 × 9 PDB declaration: nonameric |
Chain B
2–7（6 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8VML PRC2_AJ1-450 bound to H3K4me3 Deposited 2024-01-13 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain I
20–41（22 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8VNV PRC2_AJ1-450 bound to H3K36me3 with histone H3 tail engaged Deposited 2024-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain I
20–41（22 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8W9D Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Deposited 2023-09-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 7 K POTASSIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8W9E Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2 Deposited 2023-09-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 7 K POTASSIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8W9F Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3 Deposited 2023-09-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
38–135（98 aa）
Chain E
38–135（98 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.05 Å |
| 8X15 Structure of nucleosome-bound SRCAP-C in the apo state Deposited 2023-11-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric |
Chain C
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8X19 Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state Deposited 2023-11-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric |
Chain C
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 7 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8X1C Structure of nucleosome-bound SRCAP-C in the ADP-bound state Deposited 2023-11-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric |
Chain C
1–136（136 aa）
Chain G
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8XBT The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-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 4.12 Å |
| 8XBU The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-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 4.24 Å |
| 8XBW The cryo-EM structure of the RAD51 N-terminal lobe domain bound to the histone H4 tail of the nucleosome Deposited 2023-12-07 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric |
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 2.89 Å |
| 8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric |
Chain a
2–136（135 aa）
Chain e
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric |
Chain a
2–136（135 aa）
Chain e
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8Y3C Cryo-EM structure of the overlapping di-nucleosome (closed form) Deposited 2024-01-29 | Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
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 5.21 Å |
| 8Y3D Cryo-EM structure of the overlapping di-nucleosome (intermediate form2) Deposited 2024-01-29 | Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
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 5.10 Å |
| 8Y3E Cryo-EM structure of the overlapping di-nucleosome (open form) Deposited 2024-01-29 | Different experimental method 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 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.32 Å |
| 8Y3F Cryo-EM structure of the overlapping di-nucleosome (intermediate form1) Deposited 2024-01-29 | Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
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 4.54 Å |
| 8YBJ Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence Deposited 2024-02-14 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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-PROPANE
|
Resolution 2.38 Å |
| 8YBK Cryo-EM structure of the human nucleosome containing the H3.1 E97K mutant Deposited 2024-02-14 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：E97K Mutation：E97K | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.69 Å |
| 8YJF Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and an H2A-H2B dimer Deposited 2024-03-01 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain C
57–136（80 aa）
Chain E
57–136（80 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M calcium acetate, 0.1 M Sodium cacodylate pH 5.5, 12% (w/v) PEG 8000
|
Resolution 4.40 Å R-free 0.312 |
| 8YJM Structure of human SPT16 MD-CTD and MCM2 HBD chaperoning a histone H3-H4 tetramer and a single chain H2B-H2A chimera Deposited 2024-03-02 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric |
Chain C
57–136（80 aa）
Chain E
57–136（80 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.2 M sodium acetate, 0.1 M sodium citrate pH 5.5, 5%(w/v) PEG 4000
|
Resolution 4.15 Å R-free 0.286 |
| 8YNY Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome Deposited 2024-03-12 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: 13-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 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.52 Å |
| 8YTI Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2024-03-26 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-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 | CL CHLORIDE ION × 8 CA CALCIUM ION × 52 K POTASSIUM ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；40-45 mM CaCl2, 25 mM KCl, 10 mM Na-acetate (pH 4.5)
|
Resolution 2.70 Å R-free 0.267 |
| 8YV8 Cryo-EM structure of CDCA7 bound to nucleosome including hemimethylated CpG site in Widom601 positioning sequence. Deposited 2024-03-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9ECP Structure of the native human NCP purified from HEK293 cells Deposited 2024-11-14 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
39–134（96 aa）
Chain E
39–134（96 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.91 Å |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Q
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Z
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain a
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain b
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 13 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain c
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 14 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain d
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 15 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain e
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 16 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain f
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain R
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain S
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain T
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain U
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain V
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain W
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain X
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9EHI Crystal structure of ENL YEATS in complex with histone H3 methacrylated at K18 Deposited 2024-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain Y
16–22（7 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
|
Resolution 2.60 Å R-free 0.267 |
| 9FGQ Structure of human APC3loop 375-381 bound to the NCP Deposited 2024-05-24 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；20 mM HEPEs pH8.0, 50 mM NaCl, 0.5 mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 9FH9 Structure of CyclinB1 N-terminus bound to the NCP Deposited 2024-05-27 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 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 2.50 Å |
| 9GCG CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Deposited 2024-08-01 | 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 × 18 PDB declaration: 20-meric |
Chain M
1–136（136 aa）
Chain Q
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.43 Å |
| 9GE4 CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Deposited 2024-08-07 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain M
1–136（136 aa）
Chain Q
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.52 Å |
| 9GE5 CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric |
Chain M
43–136（94 aa）
Chain Q
43–136（94 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 9GEL CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric |
Chain M
1–136（136 aa）
Chain Q
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.86 Å |
| 9GEV CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric |
Chain M
1–136（136 aa）
Chain Q
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.47 Å |
| 9GF6 CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-08 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain M
1–136（136 aa）
Chain Q
1–136（136 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 |
| 9GFB CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-08 | 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 × 18 PDB declaration: 20-meric |
Chain M
1–136（136 aa）
Chain Q
1–136（136 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.55 Å |
| 9GFM CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-09 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain M
44–136（93 aa）
Chain Q
37–136（100 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 |
| 9IGW Ku70/80 bound to 147 bp nucleosome Deposited 2025-02-20 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 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 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 9IGX Ku70/80 bound to 153 bp nucleosome Deposited 2025-02-20 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain A
39–135（97 aa）
Chain E
39–135（97 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.56 Å |
| 9J8M Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (High mobility complex) Deposited 2024-08-21 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
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 3.82 Å |
| 9J8N Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (Low mobility complex) Deposited 2024-08-21 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 32-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
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 7.14 Å |
| 9J8O Cryo-EM structure of BAF-Lamin A/C IgF-H1-nucleosome complex Deposited 2024-08-21 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 28-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
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 4.05 Å |
| 9J8W Cryo-EM structure of NCP-UV-DDB complex containing CPD Deposited 2024-08-21 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 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 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.38 Å |
| 9JC6 Human H2BW2 nucleosome Deposited 2024-08-28 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.34 Å |
| 9MLL GammaH2AX containing nucleosomes, Parallel stack Deposited 2024-12-19 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain L
1–136（136 aa）
Chain P
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 3.70 Å |
| 9MLN GammaH2AX containing nucleosome, Canonical (Class 1) Deposited 2024-12-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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 3.30 Å |
| 9MLR GammaH2AX containing nucleosome, Half-wrapped (Class 2) Deposited 2024-12-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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 3.10 Å |
| 9MLS GammaH2AX containing nucleosome, Extended (Class 3) Deposited 2024-12-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
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 3.60 Å |
| 9MMK H2AX containing nucleosome, Canonical (Class 1) Deposited 2024-12-20 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9MMM H2AX containing nucleosomes, Parallel stack Deposited 2024-12-20 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain L
1–136（136 aa）
Chain P
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 9MMN H2AX containing nucleosomes, Left offset stack Deposited 2024-12-20 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain L
1–136（136 aa）
Chain P
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 9MMO H2AX containing nucleosomes, Right offset stack Deposited 2024-12-20 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain L
1–136（136 aa）
Chain P
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 9MMT H2AX containing nucleosome, Unwrapped (Class 2) Deposited 2024-12-20 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9Q80 Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome Deposited 2025-02-21 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-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 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.39 Å |
| 9Q8X Ku70/80 bound to a 153 bp H2AX nucleosome Deposited 2025-02-25 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-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 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 9Q9F DNA-PK bound to a 153 bp H2AX nucleosome model 1 Deposited 2025-02-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method 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）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.54 Å |
| 9QCR DNA-PK bound to 153 bp H2AX nucleosome model 2 Deposited 2025-03-05 | Different construct Different mutation/modification Different oligomeric state Different experimental method 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）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.37 Å |
| 9QCS Ku80 mediated DNA-PK dimer bound to 153 bp H2AX nucleosome Deposited 2025-03-05 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 26-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
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 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.38 Å |
| 9QLM Solution structure of the TAF3-PHD bound to a H3K4me3Q5ser histone tail peptide with a serotonylated glutamine Deposited 2025-03-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–13（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 2 SRO SEROTONIN × 1 |
SOLUTION NMR
NMR measurement conditions
pH 7；293 K；Ionic strength (raw mmCIF value) 44；Pressure 1
NMR sample composition
0.88 mM [U-13C; U-15N] TAF3-PHD, 0.88 mM H3K4me3Q5ser, 20 mM potassium phosphate, 4 mM potassium chloride, 10 uM zinc chloride, 0.01 % w/v sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 9QMS DNA-PK bound to 153 bp H2AX nucleosome with ATPyS Deposited 2025-03-24 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 30-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
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 5.00 Å |
| 9R04 p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample) Deposited 2025-04-24 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-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 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 9R2M p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, composite map) Deposited 2025-04-30 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-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 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9R2P p53 bound to nucleosome at position SHL+5.9 (crosslinked sample) Deposited 2025-04-30 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-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 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.18 Å |
| 9R2Q p53 bound to nucleosome at position SHL-5.7 (non-crosslinked sample) Deposited 2025-04-30 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-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 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9RL4 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2025-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | PTD PENTANEDIAL × 16 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9RMC Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1 Deposited 2025-06-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 9RN1 Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2 Deposited 2025-06-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-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 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.90 Å |
| 9RN2 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 Deposited 2025-06-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-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 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric |
Chain a
1–136（136 aa）
Chain c
1–136（136 aa）
Chain e
1–136（136 aa）
Chain g
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 3.62 Å |
| 9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric |
Chain e
1–136（136 aa）
Chain g
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 6.54 Å |
| 9UZ7 Cryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking Deposited 2025-05-16 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain B
2–136（135 aa）
|
Mutation：C96S/C110S/K115C Mutation：C96S/C110S/K115C Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6；10 mM HEPES, pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution not provided |
| 9V6Q Cryo-EM structure of two cPRC1 complexes bound to opposite faces of an endogenous 147-bp mono-nucleosome Deposited 2025-05-27 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 4.60 Å |
| 9V6S Cryo-EM structure of a single cPRC1 complex engaged on one face of an endogenous 147-bp mononucleosome Deposited 2025-05-27 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.00 Å |
| 9V6X Cryo-EM structure of the cPRC1 complex bound to an endogenous 184-bp mono-nucleosome Deposited 2025-05-27 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 4.00 Å |
| 9V8L Cryo-EM structure of the cPRC1-di-nucleosome (loose) complex Deposited 2025-05-29 | Different oligomeric state 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）
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 6.60 Å |
| 9V9H Cryo-EM structure of the cPRC1-di-nucleosome (tight) complex Deposited 2025-05-30 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain K
1–136（136 aa）
Chain M
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 4.50 Å |
| 9V9P Cryo-EM structure of the cPRC1-di-nucleosome (CBX7) complex Deposited 2025-06-01 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain K
1–136（136 aa）
Chain M
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.40 Å |
| 9VEM SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 1 Deposited 2025-06-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
17–22（6 aa）
|
Not recorded | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 2.57 Å R-free 0.264 |
| 9VEW SIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 2 Deposited 2025-06-10 | 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 C
16–22（7 aa）
|
Not recorded | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 2.68 Å R-free 0.251 |
| 9VG0 SIRT2 structure in complex with H3K18myr peptide Deposited 2025-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
16–22（7 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 5 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 1.61 Å R-free 0.231 |
| 9VG3 SIRT2 structure in complex with H3K18myr peptide: pre NAD binding state Deposited 2025-06-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
17–22（6 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 2 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；Tris 8.0, 25% PEG2000MME
|
Resolution 2.15 Å R-free 0.251 |
| 9VGE SIRT2 demyristoylation intermediate I structure Deposited 2025-06-13 | 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 C
16–22（7 aa）
|
Not recorded | NCA NICOTINAMIDE × 1 GOL GLYCEROL × 1 ZN ZINC ION × 1 YDD [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4-bis(oxidanyl)-5-tetradecoxy-oxolan-2-yl]methyl hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 2.56 Å R-free 0.282 |
| 9VGZ SIRT2-F96A structure in complex with H3K18myr peptide and native NAD Deposited 2025-06-15 | 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 C
16–22（7 aa）
|
Not recorded | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；Tris 8.0, 25% PEG 2000MME
|
Resolution 2.34 Å R-free 0.236 |
| 9VH0 SIRT2-H187A structure in complex with H3K18myr peptide and native NAD Deposited 2025-06-16 | 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 C
16–21（6 aa）
|
Not recorded | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；0.1 M MES 5.5, 9.2% PEG10000
|
Resolution 2.41 Å R-free 0.273 |
| 9VH0 SIRT2-H187A structure in complex with H3K18myr peptide and native NAD Deposited 2025-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
16–21（6 aa）
|
Not recorded | NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；0.1 M MES 5.5, 9.2% PEG10000
|
Resolution 2.41 Å R-free 0.273 |
| 9XSF Cryo-EM structure of H4S47GlcNAc nucleosome at 3.39 angstrom Deposited 2025-11-20 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.39 Å |
| 9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.50 Å |
| 9YLE State 3 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.63 Å |
| 9YLY MLL4FC bound to a nucleosome with p53 RE Deposited 2025-10-09 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information 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 mmCIF provides none of the parsed conditions | Resolution 3.77 Å |
| 9YM8 State 2 focused on PHD FYR of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 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 mmCIF provides none of the parsed conditions | Resolution 3.43 Å |
| 9YMF State 2 focused on H3 N terminal tail of MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-09 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 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 mmCIF provides none of the parsed conditions | Resolution 3.45 Å |
| 9ZEO Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1 Deposited 2025-11-30 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
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 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
402 other PDB entries and 475 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | H31_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 4–139； UniProt 1–136 Author chain E； PDBConstruct 4–139； UniProt 1–136 Author chain K； PDBConstruct 4–139； UniProt 1–136 Author chain O； PDBConstruct 4–139； UniProt 1–136 |
