Current Protein Identity：P62805
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 10XZ Non-damaged nucleosome Deposited 2026-02-12 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 10YA Nucleosome containing a nick at SHL-4 Deposited 2026-02-12 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 10YB Nucleosome containing a nick at SHL-2 Deposited 2026-02-12 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 10YC Nucleosome containing a nick at SHL-4 Deposited 2026-02-12 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 10YD Nucleosome containing a nick at SHL-6 Deposited 2026-02-12 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 10YE DNA Ligase IIIa bound to nucleosome containing a nick at SHL0 Deposited 2026-02-12 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain B
23–102（80 aa）
Chain F
23–102（80 aa）
|
Not recorded | AMP ADENOSINE MONOPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 10YF DNA Ligase IIIa bound to nucleosome containing a nick at SHL-2 (composite) Deposited 2026-02-12 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain B
23–102（80 aa）
Chain F
23–102（80 aa）
|
Not recorded | AMP ADENOSINE MONOPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution not provided |
| 10YG DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-4 (composite) Deposited 2026-02-12 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain B
23–102（80 aa）
Chain F
23–102（80 aa）
|
Not recorded | AMP ADENOSINE MONOPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution not provided |
| 10YH DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-6 (composite) Deposited 2026-02-12 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain B
23–102（80 aa）
Chain F
23–102（80 aa）
|
Not recorded | AMP ADENOSINE MONOPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 10YI XRCC1-DNA Ligase IIIa complex bound to a nucleosome containing a nick at SHL-6 (composite) Deposited 2026-02-12 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain B
23–102（80 aa）
Chain F
23–102（80 aa）
|
Not recorded | AMP ADENOSINE MONOPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 2BQZ Crystal structure of a ternary complex of the human histone methyltransferase Pr-SET7 (also known as SET8) Deposited 2005-04-28 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
17–25（9 aa）
Fragment：RESIDUES 17-25
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7；pH 7.00
|
Resolution 1.50 Å R-free 0.206 |
| 2BQZ Crystal structure of a ternary complex of the human histone methyltransferase Pr-SET7 (also known as SET8) Deposited 2005-04-28 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
17–25（9 aa）
Fragment：RESIDUES 17-25
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7；pH 7.00
|
Resolution 1.50 Å R-free 0.206 |
| 2CV5 Crystal structure of human nucleosome core particle Deposited 2005-05-31 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
0–102（103 aa）
Chain F
0–102（103 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 |
| 2LVM Solution structure of human 53BP1 tandem Tudor domains in complex with a histone H4K20me2 peptide Deposited 2012-07-07 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
15–28（14 aa）
Fragment：UNP residues 15-28
|
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) 50；Pressure ambient
NMR sample composition
1.7 mM [U-100% 13C; U-100% 15N] protein_1, 8.5 mM protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
1.7 mM [U-100% 13C; U-100% 15N] protein_1, 8.5 mM protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 100% D2O | 100% D2O
NMR sample composition
5 mM protein_1, 4 mM [U-100% 13C; U-100% 15N] protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
5 mM protein_1, 4 mM [U-100% 13C; U-100% 15N] protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 100% D2O | 100% D2O
|
Resolution not provided |
| 2RNY Complex Structures of CBP Bromodomain with H4 ack20 Peptide Deposited 2008-02-03 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
14–28（15 aa）
Fragment：UNP residues 14-28
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition
0.5mM [U-100% 13C; U-100% 15N] sodium phosphate, 100% D2O | 100% D2O
|
Resolution not provided |
| 2RS9 Solution structure of the bromodomain of human BRPF1 in complex with histone H4K5ac peptide Deposited 2011-12-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
2–11（10 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | SOLUTION NMR |
NMR measurement conditions
pH 6.5；288 K；Ionic strength (raw mmCIF value) 100；Pressure ambient
NMR sample composition
1.5 mM H4K5ac-1, 0.54 mM [U-99% 13C; U-99% 15N] Bromodomain-2, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 3A6N The nucleosome containing a testis-specific histone variant, human H3T Deposited 2009-09-04 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 2.70 Å R-free 0.264 |
| 3AFA The human nucleosome structure Deposited 2010-02-24 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 |
| 3AV1 The human nucleosome structure containing the histone variant H3.2 Deposited 2011-02-18 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, 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 0.290 |
| 3AV2 The human nucleosome structure containing the histone variant H3.3 Deposited 2011-02-18 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, 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 0.272 |
| 3AYW Crystal Structure of Human Nucleosome Core Particle Containing H3K56Q mutation Deposited 2011-05-19 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 2.90 Å R-free 0.273 |
| 3AZE Crystal Structure of Human Nucleosome Core Particle Containing H3K64Q mutation Deposited 2011-05-25 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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, 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 2.70 Å R-free 0.263 |
| 3AZG Crystal Structure of Human Nucleosome Core Particle Containing H3K115Q mutation Deposited 2011-05-25 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Mutation：K31Q Mutation：K31Q | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Mutation：K44Q Mutation：K44Q | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Mutation：K59Q Mutation：K59Q | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Mutation：K77Q Mutation：K77Q | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Mutation：K79Q Mutation：K79Q | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Mutation：K91Q Mutation：K91Q | 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 |
| 3CFS Structural basis of the interaction of RbAp46/RbAp48 with histone H4 Deposited 2008-03-04 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
28–42（15 aa）
Fragment：UNP residues 28 to 42
|
Not recorded | ARS ARSENIC × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.4；277 K；18% PEG8000, 0.2M Ca acetate, 0.1M Na Cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.40 Å R-free 0.249 |
| 3CFV Structural basis of the interaction of RbAp46/RbAp48 with histone H4 Deposited 2008-03-04 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
25–42（18 aa）
Fragment：UNP residues 25 to 42
|
Not recorded | ARS ARSENIC × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；13% PEG 2000, 0.2M Ca acetate, 0.1M Na Cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.60 Å R-free 0.257 |
| 3CFV Structural basis of the interaction of RbAp46/RbAp48 with histone H4 Deposited 2008-03-04 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
25–42（18 aa）
Fragment：UNP residues 25 to 42
|
Not recorded | ARS ARSENIC × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；13% PEG 2000, 0.2M Ca acetate, 0.1M Na Cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.60 Å R-free 0.257 |
| 3F9W Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20 / AdoHcy Deposited 2008-11-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
16–25（10 aa）
Fragment：UNP residues 16-25
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.60 Å R-free 0.206 |
| 3F9W Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20 / AdoHcy Deposited 2008-11-14 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
16–25（10 aa）
Fragment：UNP residues 16-25
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.60 Å R-free 0.206 |
| 3F9W Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20 / AdoHcy Deposited 2008-11-14 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain G
16–25（10 aa）
Fragment：UNP residues 16-25
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.60 Å R-free 0.206 |
| 3F9W Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20 / AdoHcy Deposited 2008-11-14 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
16–25（10 aa）
Fragment：UNP residues 16-25
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.60 Å R-free 0.206 |
| 3F9X Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me2 / AdoHcy Deposited 2008-11-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
16–25（10 aa）
Fragment：UNP residues 16-25
|
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；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.25 Å R-free 0.207 |
| 3F9X Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me2 / AdoHcy Deposited 2008-11-14 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
16–25（10 aa）
Fragment：UNP residues 16-25
|
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；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.25 Å R-free 0.207 |
| 3F9X Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me2 / AdoHcy Deposited 2008-11-14 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain G
16–25（10 aa）
Fragment：UNP residues 16-25
|
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；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.25 Å R-free 0.207 |
| 3F9X Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me2 / AdoHcy Deposited 2008-11-14 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
16–25（10 aa）
Fragment：UNP residues 16-25
|
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；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.25 Å R-free 0.207 |
| 3F9Y Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me1 / AdoHcy Deposited 2008-11-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
16–25（10 aa）
Fragment：UNP residues 16-25
|
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；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.50 Å R-free 0.220 |
| 3F9Y Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20me1 / AdoHcy Deposited 2008-11-14 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
16–25（10 aa）
Fragment：UNP residues 16-25
|
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；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.50 Å R-free 0.220 |
| 3F9Z Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy Deposited 2008-11-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
16–25（10 aa）
Fragment：UNP residues 16-25
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.60 Å R-free 0.257 |
| 3F9Z Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy Deposited 2008-11-14 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
16–25（10 aa）
Fragment：UNP residues 16-25
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.60 Å R-free 0.257 |
| 3F9Z Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy Deposited 2008-11-14 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain G
16–25（10 aa）
Fragment：UNP residues 16-25
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.60 Å R-free 0.257 |
| 3F9Z Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y245F / H4-Lys20 / AdoHcy Deposited 2008-11-14 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
16–25（10 aa）
Fragment：UNP residues 16-25
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25% Pentaerythritol ethoxylate, 50mM Ammonium sulfate, 50mM Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.60 Å R-free 0.257 |
| 3NQJ Crystal structure of (CENP-A/H4)2 heterotetramer Deposited 2010-06-29 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
21–103（83 aa）
Fragment：UNP residues 21-103
|
Not recorded | PO4 PHOSPHATE ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.17 M ammonium sulfate, 0.085 M sodium cacodylate (pH 6.5), 25.5% PEG-8000, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.10 Å R-free 0.241 |
| 3NQU Crystal structure of partially trypsinized (CENP-A/H4)2 heterotetramer Deposited 2010-06-29 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
1–103（103 aa）
|
Not recorded | SO4 SULFATE ION × 10 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.9；295 K；2 M ammonium sulfate, 0.1 M HEPES (pH 7.9), VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.50 Å R-free 0.302 |
| 3O36 Crystal structure of TRIM24 PHD-Bromo complexed with H4(14-19)K16ac peptide Deposited 2010-07-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
15–20（6 aa）
Fragment：UNP residues 15-20
|
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 6.5；293 K；50 mM Bis-Tris (pH 6.5), 30% Polyethylene glycol 3350, 100 mM ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.216 |
| 3O36 Crystal structure of TRIM24 PHD-Bromo complexed with H4(14-19)K16ac peptide Deposited 2010-07-23 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
15–20（6 aa）
Fragment：UNP residues 15-20
|
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 6.5；293 K；50 mM Bis-Tris (pH 6.5), 30% Polyethylene glycol 3350, 100 mM ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.216 |
| 3QZS Crystal Structure of BPTF bromo in complex with histone H4K16ac - Form I Deposited 2011-03-07 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
13–22（10 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；100 mM Tris-HCl pH 8.0, 20% Glycerol, vapor diffusion, hanging drop
|
Resolution 1.80 Å R-free 0.230 |
| 3QZS Crystal Structure of BPTF bromo in complex with histone H4K16ac - Form I Deposited 2011-03-07 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
13–22（10 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；100 mM Tris-HCl pH 8.0, 20% Glycerol, vapor diffusion, hanging drop
|
Resolution 1.80 Å R-free 0.230 |
| 3QZT Crystal Structure of BPTF bromo in complex with histone H4K16ac - Form II Deposited 2011-03-07 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
13–22（10 aa）
|
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；293 K；20% (W/V) PEGMME 2K, 20% Glycerol and 0.2 M KCl, 0.1 M Tris-HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.50 Å R-free 0.198 |
| 3QZV Crystal Structure of BPTF PHD-linker-bromo in complex with histone H4K12ac peptide Deposited 2011-03-07 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
8–18（11 aa）
Fragment：Histone H4 7-17
|
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 7.5；293 K；20% (W/V) PEG3000, 0.3 M NaAcetate, 0.1 M Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.234 |
| 3R45 Structure of a CENP-A-Histone H4 Heterodimer in complex with chaperone HJURP Deposited 2011-03-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–103（103 aa）
|
Not recorded | SO4 SULFATE ION × 13 GOL GLYCEROL × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；2M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.60 Å R-free 0.245 |
| 3UVW Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K5acK8ac) Deposited 2011-11-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
2–12（11 aa）
Fragment：unp residues 2-12
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；278 K；0.1M Tris, 20% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 278K, pH 8.0
|
Resolution 1.37 Å R-free 0.171 |
| 3UVY Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K16acK20ac) Deposited 2011-11-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
16–26（11 aa）
Fragment：UNP RESIDUES 16-26
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；278 K；0.2M NaI, 0.1M BTProp, 20% PEG 3350, 10% EtGly, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K
|
Resolution 2.02 Å R-free 0.258 |
| 3UW9 Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K8acK12ac) Deposited 2011-12-01 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain E
8–18（11 aa）
Fragment：unp residues 8-18
|
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 8；277 K；0.1M Tris, 0.3M LiCl
15% PEG6000, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 8.0
|
Resolution 2.30 Å R-free 0.257 |
| 3UW9 Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K8acK12ac) Deposited 2011-12-01 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain F
8–18（11 aa）
Fragment：unp residues 8-18
|
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 8；277 K；0.1M Tris, 0.3M LiCl
15% PEG6000, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 8.0
|
Resolution 2.30 Å R-free 0.257 |
| 3W96 Crystal Structure of Human Nucleosome Core Particle lacking H2A N-terminal region Deposited 2013-04-01 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 3.42 Å R-free 0.303 |
| 3W99 Crystal Structure of Human Nucleosome Core Particle lacking H4 N-terminal region Deposited 2013-04-01 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
17–103（87 aa）
Fragment：UNP residues 17-103
Chain F
17–103（87 aa）
Fragment：UNP residues 17-103
|
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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 |
| 3WTP Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3 Deposited 2014-04-14 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, vapor diffusion, hanging drop, temperature 293K
|
Resolution 2.67 Å R-free 0.270 |
| 3X1S Crystal structure of the nucleosome core particle Deposited 2014-11-27 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | MN MANGANESE (II) ION × 6 CL CHLORIDE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 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 |
| 4GQB Crystal Structure of the human PRMT5:MEP50 Complex Deposited 2012-08-22 | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count |
Chain C
2–22（21 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 0XU (2S,5S,6E)-2,5-diamino-6-[(3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxydihydrofuran-2(3H)-ylidene]hexanoic acid × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20-30% PEG3350, 100-250 mM ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.06 Å R-free 0.222 |
| 4H9N Complex structure 1 of DAXX/H3.3(sub5)/H4 Deposited 2012-09-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
2–103（102 aa）
|
Not recorded | PO4 PHOSPHATE ION × 9 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.95 Å R-free 0.209 |
| 4H9O Complex structure 2 of DAXX/H3.3(sub5,G90M)/H4 Deposited 2012-09-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
2–103（102 aa）
|
Not recorded | PO4 PHOSPHATE ION × 10 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.05 Å R-free 0.225 |
| 4H9P Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
2–103（102 aa）
|
Not recorded | PO4 PHOSPHATE ION × 7 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.8 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.242 |
| 4H9P Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain B
2–103（102 aa）
|
Not recorded | PO4 PHOSPHATE ION × 14 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.8 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.242 |
| 4H9Q Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4 Deposited 2012-09-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
2–103（102 aa）
|
Not recorded | PO4 PHOSPHATE ION × 9 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.95 Å R-free 0.221 |
| 4H9Q Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4 Deposited 2012-09-24 | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain B
2–103（102 aa）
|
Not recorded | PO4 PHOSPHATE ION × 18 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.95 Å R-free 0.221 |
| 4H9R Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
2–103（102 aa）
|
Not recorded | PO4 PHOSPHATE ION × 6 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.6 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.230 |
| 4H9R Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain B
2–103（102 aa）
|
Not recorded | PO4 PHOSPHATE ION × 12 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.6 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.230 |
| 4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
21–103（83 aa）
|
Not recorded | PO4 PHOSPHATE ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.60 Å R-free 0.250 |
| 4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain D
21–103（83 aa）
|
Not recorded | PO4 PHOSPHATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.60 Å R-free 0.250 |
| 4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24 | Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain C
21–103（83 aa）
Chain D
21–103（83 aa）
|
Not recorded | PO4 PHOSPHATE ION × 5 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.60 Å R-free 0.250 |
| 4HGA Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX Deposited 2012-10-07 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–103（103 aa）
|
Not recorded | PC4 TETRACHLOROPLATINATE(II) × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.6；298 K；0.1M HEPES-Na, pH 7.6, 23% (v/v) PEG 3350, 0.25M Ammonium acetate, 1% Tacsimate pH 7.0, 6% ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.80 Å R-free 0.271 |
| 4M38 Crystal structure of Trypanosoma brucei protein arginine methyltransferase 7 complex with AdoHcy and histone H4 peptide Deposited 2013-08-06 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain E
2–22（21 aa）
Fragment：UNP residues 2-22
Chain F
2–22（21 aa）
Fragment：UNP residues 2-22
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；100mM MES, 20% PEG 1000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.20 Å R-free 0.230 |
| 4QUT Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) complexed with Histone H4-K(ac)12 Deposited 2014-07-12 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
7–13（7 aa）
Fragment：histone H4 tail
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 11 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277.15 K；apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 28-32% PEG 3350, 50 mM bis-tris pH 5.5, 50 mM ammonium phosphate and 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
|
Resolution 1.70 Å R-free 0.180 |
| 4QUU Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) complexed with Histone H4-K(ac)5 Deposited 2014-07-12 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
1–13（13 aa）
Fragment：histone H4 tail
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 9 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277.15 K；apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 28-32% PEG 3350, 50 mM bis-tris pH 5.5, 50 mM ammonium phosphate and 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
|
Resolution 1.80 Å R-free 0.200 |
| 4QYD Crystal Structure of the human BRPF1 bromodomain in complex with a histone H4K12ac peptide Deposited 2014-07-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
5–18（14 aa）
Fragment：histone H4K12ac peptide (UNP residues 5-18)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
pH 7.5；277 K；0.1 M HEPES, pH 7.5, 10% w/v polyethylene glycol (PEG) 6,000, 5% v/v (+/-)-2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.94 Å R-free 0.213 |
| 4YM5 Crystal structure of the human nucleosome containing 6-4PP (inside) Deposited 2015-03-06 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 3.51 Å R-free 0.287 |
| 4YY6 Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain Z
2–12（11 aa）
Fragment：N-terminal tail (UNP residues 2-12)
|
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 4；277 K；0.2 M sodium malonate, pH 4.0, 20% w/v PEG3350
|
Resolution 1.45 Å R-free 0.208 |
| 4YYD Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain Z
2–12（11 aa）
Fragment：N-terminal tail (UNP residues 2-12)
|
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 7；277 K；0.2 M sodium malonate, pH 7.0, 20% w/v PEG3350
|
Resolution 1.52 Å R-free 0.226 |
| 4YYG Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
2–12（11 aa）
Fragment：N-terminal tail (UNP residues 2-12)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.05 M calcium chloride dihydrate, 0.1 M Bis-Tris, pH 6.5, 30% v/v PEG550 MME
|
Resolution 2.10 Å R-free 0.311 |
| 4YYH Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain Z
2–12（11 aa）
Fragment：N-terminal tail (UNP residues 2-12)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M sodium citrate, pH 5.5, 0.2 M sodium chloride, 20% w/v PEG3350
|
Resolution 1.74 Å R-free 0.260 |
| 4YYH Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-23 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain Y
2–12（11 aa）
Fragment：N-terminal tail (UNP residues 2-12)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M sodium citrate, pH 5.5, 0.2 M sodium chloride, 20% w/v PEG3350
|
Resolution 1.74 Å R-free 0.260 |
| 4YYI Crystal structure of BRD9 Bromodomain bound to an acetylated peptide Deposited 2015-03-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
2–12（11 aa）
Fragment：N-terminal tail (UNP residues 2-12)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M Bis-Tris, pH 6.5, 25% w/v PEG3350
|
Resolution 1.50 Å R-free 0.242 |
| 4YYI Crystal structure of BRD9 Bromodomain bound to an acetylated peptide Deposited 2015-03-23 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain F
2–12（11 aa）
Fragment：N-terminal tail (UNP residues 2-12)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M Bis-Tris, pH 6.5, 25% w/v PEG3350
|
Resolution 1.50 Å R-free 0.242 |
| 4YYJ Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
2–12（11 aa）
Fragment：N-terminal tail (UNP residues 2-12)
|
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 7.5；277 K；0.2 M ammonium chloride, 20% w/v PEG3350
|
Resolution 1.85 Å R-free 0.244 |
| 4YYJ Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain F
2–12（11 aa）
Fragment：N-terminal tail (UNP residues 2-12)
|
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 7.5；277 K；0.2 M ammonium chloride, 20% w/v PEG3350
|
Resolution 1.85 Å R-free 0.244 |
| 4YYK Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
2–12（11 aa）
Fragment：N-terminal tail (UNP residues 2-12)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M MES, pH 6.5, 15% w/v PEG550 MME
|
Resolution 1.79 Å R-free 0.261 |
| 4YYK Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-24 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain F
2–12（11 aa）
Fragment：N-terminal tail (UNP residues 2-12)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M MES, pH 6.5, 15% w/v PEG550 MME
|
Resolution 1.79 Å R-free 0.261 |
| 4YYM Crystal structure of TAF1 BD2 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain Z
2–12（11 aa）
Fragment：N-terminal tail (UNP residues 2-12)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CA CALCIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M calcium chloride, 20 w/v PEG3350
|
Resolution 1.50 Å R-free 0.261 |
| 4YYN Crystal structure of TAF1 BD2 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain Z
2–12（11 aa）
Fragment：N-terminal tail (UNP residues 2-12)
|
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 7.5；277 K；0.2 M calcium acetate, 20% w/v PEG3350
|
Resolution 1.85 Å R-free 0.243 |
| 4Z2M Crystal structure of human SPT16 Mid-AID/H3-H4 tetramer FACT Histone complex Deposited 2015-03-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain H
1–103（103 aa）
Chain J
1–103（103 aa）
|
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 |
| 4Z5T The nucleosome containing human H3.5 Deposited 2015-04-03 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.80 Å R-free 0.269 |
| 5AV5 human nucleosome core particle Deposited 2015-06-11 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 |
| 5AY8 Crystal structure of human nucleosome containing H3.Y Deposited 2015-08-10 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | MN MANGANESE (II) ION × 8 CL CHLORIDE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；sodium acetate, manganese chloride, 2-propanol, trimethylamine N-oxide
|
Resolution 2.80 Å R-free 0.249 |
| 5B0Y Crystal structure of the nucleosome containing histone H3 with the crotonylated lysine 122 Deposited 2015-11-13 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | 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 2.56 Å R-free 0.249 |
| 5B0Z The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution Deposited 2015-11-14 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 3 | 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 0.254 |
| 5B24 The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer Deposited 2015-12-31 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 |
| 5B32 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3. Deposited 2016-02-08 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 2.35 Å R-free 0.259 |
| 5B33 The crystal structure of the H2AZ nucleosome with H3.3. Deposited 2016-02-08 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.92 Å R-free 0.252 |
| 5B40 The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations Deposited 2016-03-22 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Mutation：K31C Mutation：K31C | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；90mM Tris-HCl (pH 7.8), 3.6% PGA-LM, 25.2% PEG 400, 2-6% Pentaerythritol ethoxylate (3/4 EO/OH)
|
Resolution 3.33 Å R-free 0.263 |
| 5BNV Crystal structure of Human MCM2 HBD chaperoning a histone H3-H4 tetramer Deposited 2015-05-26 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain B
2–103（102 aa）
Chain E
2–103（102 aa）
|
Not recorded | PO4 PHOSPHATE ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5 M sodium/potassium phosphate, pH 8.0
|
Resolution 2.79 Å R-free 0.220 |
| 5BNX Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.3-H4 dimer Deposited 2015-05-26 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
2–103（102 aa）
|
Not recorded | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；3.2 M sodium formate, 0.1 M Tris, pH 8.5
|
Resolution 2.31 Å R-free 0.213 |
| 5BO0 Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.2-H4 dimer Deposited 2015-05-26 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
2–103（102 aa）
|
Not recorded | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；3.2 M sodium formate, 0.1 M Tris, pH 8.5
|
Resolution 2.91 Å R-free 0.238 |
| 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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain K
1–103（103 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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
1–103（103 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 | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain G
1–103（103 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 | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain O
1–103（103 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 | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain S
1–103（103 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 | Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain W
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.63 Å R-free 0.284 |
| 5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count |
Chain C
2–21（20 aa）
Fragment：DNA binding residues 2-21
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
|
Resolution 2.34 Å R-free 0.221 |
| 5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain C
2–21（20 aa）
Fragment：DNA binding residues 2-21
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
|
Resolution 2.34 Å R-free 0.221 |
| 5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 | Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain C
2–21（20 aa）
Fragment：DNA binding residues 2-21
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
|
Resolution 2.34 Å R-free 0.221 |
| 5FA5 Crystal Structure of PRMT5:MEP50 in complex with MTA and H4 peptide Deposited 2015-12-10 | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
2–21（20 aa）
Fragment：DNA binding residues 2-21
|
Not recorded | MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；281 K；200 mM ammonium sulfate, 20-28% PEG 3350, 2 mM 5-deoxy-5-(methylthio)adenosine, 1 mM H4 peptide (1-20)
|
Resolution 2.34 Å R-free 0.221 |
| 5FWE JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15)R3me2s PEPTIDE Deposited 2016-02-15 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
2–16（15 aa）
Fragment：HISTONE H4(1-15)R3ME2S PEPTIDE, UNP RESIDUES 2-16
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；SITTING DROPS, 277 K, 0.15 M POTASSIUM BROMIDE, 30 % W/V PEG 2000 MME, pH 7.5
|
Resolution 2.05 Å R-free 0.255 |
| 5FWE JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15)R3me2s PEPTIDE Deposited 2016-02-15 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
2–16（15 aa）
Fragment：HISTONE H4(1-15)R3ME2S PEPTIDE, UNP RESIDUES 2-16
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 OGA N-OXALYLGLYCINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；SITTING DROPS, 277 K, 0.15 M POTASSIUM BROMIDE, 30 % W/V PEG 2000 MME, pH 7.5
|
Resolution 2.05 Å R-free 0.255 |
| 5GSE Crystal structure of unusual nucleosome Deposited 2016-08-16 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | 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 |
| 5GSU Crystal structure of nucleosome core particle consisting of human testis-specific histone variants, Th2A and Th2B Deposited 2016-08-17 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 |
| 5GXQ The crystal structure of the nucleosome containing H3.6 Deposited 2016-09-19 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.85 Å R-free 0.262 |
| 5JA4 Crystal structure of human TONSL and MCM2 HBDs binding to a histone H3-H4 tetramer Deposited 2016-04-11 | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count |
Chain B
2–103（102 aa）
|
Not recorded | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 GOL GLYCEROL × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；0.1M MES pH 5.6, 7% isopropanol
|
Resolution 2.42 Å R-free 0.246 |
| 5JRG Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF) Deposited 2016-05-06 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 |
| 5KDM Crystal structure of EBV tegument protein BNRF1 in complex with histone chaperone DAXX and histones H3.3-H4 Deposited 2016-06-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；0.1M MES pH 6.0, 0.8 M ammonium sulfate
|
Resolution 3.50 Å R-free 0.280 |
| 5X7X The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution Deposited 2017-02-27 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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
|
Resolution 2.18 Å R-free 0.256 |
| 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 |
| 5Y0C Crystal Structure of the human nucleosome at 2.09 angstrom resolution Deposited 2017-07-16 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | 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 |
| 6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric（25） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.60 Å |
| 6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 9.90 Å |
| 6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.00 Å |
| 6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.70 Å |
| 6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.70 Å |
| 6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric（25） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.60 Å |
| 6BUZ Cryo-EM structure of CENP-A nucleosome in complex with kinetochore protein CENP-N Deposited 2017-12-11 | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.92 Å |
| 6C0W Cryo-EM structure of human kinetochore protein CENP-N with the centromeric nucleosome containing CENP-A Deposited 2018-01-02 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–102（102 aa）
Chain F
1–102（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 6E0C Cryo-EM structure of the CENP-A nucleosome (W601) in complex with a single chain antibody fragment Deposited 2018-07-06 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.63 Å |
| 6E0P Cryo-EM structure of the centromeric nucleosome (Native alpha satellite DNA) in complex with a single chain antibody fragment Deposited 2018-07-06 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 sec before plunging
|
Resolution 2.60 Å |
| 6FML CryoEM Structure INO80core Nucleosome complex Deposited 2018-01-31 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain N
2–103（102 aa）
Chain R
2–103（102 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8；20 mM HEPES pH 8,
60 mM KCl,
0.5% glycerol,
0.25 mM CaCl2,
20 uM ZnCl2,
0.25 mM DTT,
0.05% Octyl-beta-glucoside
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.34 Å |
| 6HKT Structure of an H1-bound 6-nucleosome array Deposited 2018-09-08 | Assembly 1 Protein–DNA Heteromer；Protein × 48 PDB declaration: 50-meric（50） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
Chain V
1–103（103 aa）
Chain Z
1–103（103 aa）
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
Chain l
1–103（103 aa）
Chain p
1–103（103 aa）
Chain v
1–103（103 aa）
Chain z
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric（19） Consistent with all polymers |
Chain J
1–103（103 aa）
Chain N
1–103（103 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 |
| 6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric（25） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.90 Å |
| 6IPU Human nucleosome core particle containing 145 bp of DNA Deposited 2018-11-04 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
22–103（82 aa）
Chain F
17–103（87 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
22–103（82 aa）
Chain F
17–103（87 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 |
| 6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.90 Å |
| 6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 | Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric（27） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 | Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric（27） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.70 Å |
| 6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric（28） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 6JOU Crystal structure of the human nucleosome containing H2A.Z.1 S42R Deposited 2019-03-23 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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
|
Resolution 2.50 Å R-free 0.253 |
| 6JR1 Crystal structure of the human nucleosome phased with 16 selenium atoms Deposited 2019-04-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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
|
Resolution 2.40 Å R-free 0.243 |
| 6JXD Human nucleosome core particle with cohesive end DNA termini Deposited 2019-04-23 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
22–103（82 aa）
Chain F
17–103（87 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
17–103（87 aa）
Chain F
17–103（87 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 |
| 6KXV Crystal structure of a nucleosome containing Leishmania histone H3 Deposited 2019-09-13 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；sodium acetate, isopropanol, manganese chloride, trimethylamine N-oxide
|
Resolution 3.63 Å R-free 0.264 |
| 6L49 H3-CA-H3 tri-nucleosome with the 22 base-pair linker DNA Deposited 2019-10-16 | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
Chain T
1–103（103 aa）
Chain X
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
Chain T
1–103（103 aa）
Chain X
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
17–103（87 aa）
Chain F
17–103（87 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 | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric（19） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 38-meric（38） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
Chain V
1–103（103 aa）
Chain Z
1–103（103 aa）
Chain f
1–103（103 aa）
Chain j
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric（19） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric（22） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
17–103（87 aa）
Chain F
17–103（87 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain L
1–103（103 aa）
Chain P
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric（18） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric（18） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 6M4H Structural mechanism of nucleosome dynamics governed by human histone variants H2A.B and H2A.Z.2.2 Deposited 2020-03-07 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 6MLC PHD6 domain of MLL3 in complex with histone H4 Deposited 2018-09-27 | Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric（18） Consistent with protein count |
Chain E
2–21（20 aa）
Fragment：residues 2-21
|
Not recorded | ZN ZINC ION × 42 GOL GLYCEROL × 6 UNX UNKNOWN LIGAND × 30 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；2 M Na-Form, 0.1 M Tris, pH 8.5
|
Resolution 1.80 Å R-free 0.216 |
| 6MLC PHD6 domain of MLL3 in complex with histone H4 Deposited 2018-09-27 | Assembly 2 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric（18） Consistent with protein count |
Chain F
2–21（20 aa）
Fragment：residues 2-21
|
Not recorded | ZN ZINC ION × 42 GOL GLYCEROL × 24 UNX UNKNOWN LIGAND × 12 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；2 M Na-Form, 0.1 M Tris, pH 8.5
|
Resolution 1.80 Å R-free 0.216 |
| 6MUO CENP-A nucleosome bound by two copies of CENP-C(CD) and one copy CENP-N(NT) Deposited 2018-10-23 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
9–102（94 aa）
Chain F
9–102（94 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；10 mM HEPES, 50 mN NaCl, 1 mM EDTA, 1mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 8 seconds before plunging
|
Resolution 3.60 Å |
| 6MUP CENP-A nucleosome bound by two copies of CENP-C(CD) and two copies CENP-N(NT) Deposited 2018-10-23 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain B
9–102（94 aa）
Chain F
9–102（94 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；10 mM HEPES, 50 mN NaCl, 1 mM EDTA, 1mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 8 seconds before plunging
|
Resolution 3.50 Å |
| 6O1D Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA Deposited 2019-02-19 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 sec before plunging
|
Resolution 3.40 Å |
| 6R0C Human-D02 Nucleosome Core Particle with biotin-streptavidin label Deposited 2019-03-12 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 6R8Y Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Deposited 2019-04-02 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 6R8Z Cryo-EM structure of NCP_THF2(-1)-UV-DDB Deposited 2019-04-02 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 6R90 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A Deposited 2019-04-02 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 6R91 Cryo-EM structure of NCP_THF2(-3)-UV-DDB Deposited 2019-04-02 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 6R92 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B Deposited 2019-04-02 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 6R93 Cryo-EM structure of NCP-6-4PP Deposited 2019-04-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 6R94 Cryo-EM structure of NCP_THF2(-3) Deposited 2019-04-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 6RNY PFV intasome - nucleosome strand transfer complex Deposited 2019-05-09 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: octadecameric（18） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | MG MAGNESIUM ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE；1 min incubation 3.5s blot
|
Resolution 3.90 Å |
| 6RXS Crystal structure of CobB Ac3(A76G,Y92A, I131L, V187Y) in complex with H4K16-Acetyl peptide Deposited 2019-06-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
13–23（11 aa）
Fragment：H4K16Ac
|
Mutation：K16ALY Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 GOL GLYCEROL × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350
|
Resolution 1.60 Å R-free 0.205 |
| 6SE0 Class 1 : CENP-A nucleosome Deposited 2019-07-29 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 6SE6 Class2 : CENP-A nucleosome in complex with CENP-C central region Deposited 2019-07-29 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 6SEE Class2A : CENP-A nucleosome in complex with CENP-C central region Deposited 2019-07-29 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 6SEF Class2C : CENP-A nucleosome in complex with CENP-C central region Deposited 2019-07-29 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 6SEG Class1: CENP-A nucleosome in complex with CENP-C central region Deposited 2019-07-30 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 6T79 Structure of a human nucleosome at 3.2 A resolution Deposited 2019-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
|
Resolution 3.20 Å |
| 6T7A Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
|
Resolution 3.70 Å |
| 6T7B Structure of human Sox2 transcription factor in complex with a nucleosome Deposited 2019-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
|
Resolution 5.10 Å |
| 6T7C Structure of two copies of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
|
Resolution 4.00 Å |
| 6T7D Structure of human Sox11 transcription factor in complex with a nucleosome Deposited 2019-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.
|
Resolution 4.40 Å |
| 6T90 OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2019-10-25 | Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.49 Å |
| 6UPK Structure of FACT_subnucleosome complex 1 Deposited 2019-10-17 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.90 Å |
| 6UPL Structure of FACT_subnucleosome complex 2 Deposited 2019-10-17 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.40 Å |
| 6USJ Structure of two nucleosomes bridged by human PARP2 Deposited 2019-10-27 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric（22） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 |
| 6V92 RSC-NCP Deposited 2019-12-13 | Assembly 1 Protein–DNA Heteromer；Protein × 33 PDB declaration: 35-meric（35） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 20.00 Å |
| 6VO5 Crystal structure of Human histone acetytransferas 1 (HAT1) in complex with isobutryl-COA and K12A mutant variant of histone H4 Deposited 2020-01-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
2–21（20 aa）
|
Not recorded | ACT ACETATE ION × 1 CO6 ISOBUTYRYL-COENZYME A × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 9 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；12% PEG 20K and 0.1M MES pH6.5
|
Resolution 1.60 Å R-free 0.198 |
| 6VO5 Crystal structure of Human histone acetytransferas 1 (HAT1) in complex with isobutryl-COA and K12A mutant variant of histone H4 Deposited 2020-01-30 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
2–21（20 aa）
|
Not recorded | CO6 ISOBUTYRYL-COENZYME A × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 7 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；12% PEG 20K and 0.1M MES pH6.5
|
Resolution 1.60 Å R-free 0.198 |
| 6X59 The mouse cGAS catalytic domain binding to human assembled nucleosome Deposited 2020-05-25 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 6X5A The mouse cGAS catalytic domain binding to human nucleosome that purified from HEK293T cells Deposited 2020-05-25 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.36 Å |
| 6XJD Two mouse cGAS catalytic domain binding to human assembled nucleosome Deposited 2020-06-23 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.80 Å |
| 6Y5D Structure of human cGAS (K394E) bound to the nucleosome Deposited 2020-02-25 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric（22） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain N
1–103（103 aa）
Chain R
1–103（103 aa）
|
Not recorded | PTD PENTANEDIAL × 9 ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 6Y5E Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex) Deposited 2020-02-25 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
23–103（81 aa）
Chain F
21–103（83 aa）
|
Not recorded | PTD PENTANEDIAL × 8 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.15 Å |
| 6YOV OCT4-SOX2-bound nucleosome - SHL+6 Deposited 2020-04-15 | Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | PTD PENTANEDIAL × 8 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 7A08 CryoEM Structure of cGAS Nucleosome complex Deposited 2020-08-07 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain e
2–103（102 aa）
Chain i
2–103（102 aa）
|
Not recorded | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.11 Å |
| 7BWD Structure of Dot1L-H2BK34ub Nucleosome Complex Deposited 2020-04-14 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 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 |
| 7BXT The cryo-EM structure of CENP-A nucleosome in complex with CENP-C peptide and CENP-N N-terminal domain Deposited 2020-04-20 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7BY0 The cryo-EM structure of CENP-A nucleosome in complex with the phosphorylated CENP-C Deposited 2020-04-21 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–102（102 aa）
Chain F
1–102（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 7C0M Human cGAS-nucleosome complex Deposited 2020-05-01 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric（22） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
Chain b
2–103（102 aa）
Chain f
2–103（102 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7CIZ Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
2–103（102 aa）
|
Not recorded | SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.
|
Resolution 1.80 Å R-free 0.214 |
| 7CIZ Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-08 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.
|
Resolution 1.80 Å R-free 0.214 |
| 7CIZ Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-08 | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain J
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.
|
Resolution 1.80 Å R-free 0.214 |
| 7CJ0 Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-09 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain F
2–103（102 aa）
|
Not recorded | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M Sodium acetate, 0.1 M Tris, pH8.5, 25% (v/v) PEG 4000, 20% (v/v) Glycerol
|
Resolution 2.50 Å R-free 0.295 |
| 7CJ0 Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-09 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M Sodium acetate, 0.1 M Tris, pH8.5, 25% (v/v) PEG 4000, 20% (v/v) Glycerol
|
Resolution 2.50 Å R-free 0.295 |
| 7COW 353 bp di-nucleosome harboring cohesive DNA termini with linker histone H1.0 Deposited 2020-08-05 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.15 Å |
| 7D20 Cryo-EM structure of SET8-CENP-A-nucleosome complex Deposited 2020-09-15 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7DBP Linker histone defines structure and self-association behaviour of the 177 bp human chromosome Deposited 2020-10-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 7E8D NSD2 E1099K mutant bound to nucleosome Deposited 2021-03-01 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 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 |
| 7EIC Crystal structure of AF9 YEATS domain in complex with H4K5acK8ac peptide Deposited 2021-03-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
2–13（12 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Bis-Tris buffer (pH 6.5) containing 100 mM ammonium acetate and 25% PEG3350
|
Resolution 1.95 Å R-free 0.205 |
| 7JO9 1:1 cGAS-nucleosome complex Deposited 2020-08-06 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7JOA 2:1 cGAS-nucleosome complex Deposited 2020-08-06 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7JZV Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome Deposited 2020-09-02 | Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain Q
2–103（102 aa）
Chain q
2–103（102 aa）
|
Not recorded | ZN ZINC ION × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7K5X Cryo-EM structure of a chromatosome containing human linker histone H1.0 Deposited 2020-09-17 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.93 Å |
| 7K5Y Cryo-EM structure of a chromatosome containing human linker histone H1.4 Deposited 2020-09-17 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.76 Å |
| 7K60 Cryo-EM structure of a chromatosome containing human linker histone H1.10 Deposited 2020-09-17 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.12 Å |
| 7K61 Cryo-EM structure of 197bp nucleosome aided by scFv Deposited 2020-09-17 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.85 Å |
| 7K63 Cryo-EM structure of a chromatosome containing chimeric linker histone gH1.10-ncH1.4 Deposited 2020-09-18 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.03 Å |
| 7LMK Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3 Deposited 2021-02-05 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
15–27（13 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；13% PEG1500, 20 mM DTT and 200 mM L-proline, 0.1 M HEPES (pH 7.5)
|
Resolution 2.65 Å R-free 0.258 |
| 7LMK Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3 Deposited 2021-02-05 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain G
15–27（13 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；13% PEG1500, 20 mM DTT and 200 mM L-proline, 0.1 M HEPES (pH 7.5)
|
Resolution 2.65 Å R-free 0.258 |
| 7LMK Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3 Deposited 2021-02-05 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
15–27（13 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；13% PEG1500, 20 mM DTT and 200 mM L-proline, 0.1 M HEPES (pH 7.5)
|
Resolution 2.65 Å R-free 0.258 |
| 7LMK Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me3 Deposited 2021-02-05 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain I
15–27（13 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；13% PEG1500, 20 mM DTT and 200 mM L-proline, 0.1 M HEPES (pH 7.5)
|
Resolution 2.65 Å R-free 0.258 |
| 7LMM Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2 Deposited 2021-02-05 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
15–27（13 aa）
|
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 6.5；277 K；0.1 M MES (pH 6.5) ,13% PEG1500, 20 mM DTT and 200 mM L-proline
|
Resolution 2.80 Å R-free 0.267 |
| 7LMM Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2 Deposited 2021-02-05 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain G
15–27（13 aa）
|
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 6.5；277 K；0.1 M MES (pH 6.5) ,13% PEG1500, 20 mM DTT and 200 mM L-proline
|
Resolution 2.80 Å R-free 0.267 |
| 7LMM Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2 Deposited 2021-02-05 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain I
15–27（13 aa）
|
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 6.5；277 K；0.1 M MES (pH 6.5) ,13% PEG1500, 20 mM DTT and 200 mM L-proline
|
Resolution 2.80 Å R-free 0.267 |
| 7LMM Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2 Deposited 2021-02-05 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
15–27（13 aa）
|
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 6.5；277 K；0.1 M MES (pH 6.5) ,13% PEG1500, 20 mM DTT and 200 mM L-proline
|
Resolution 2.80 Å R-free 0.267 |
| 7LYA Cryo-EM structure of the human nucleosome core particle with linked histone proteins H2A and H2B Deposited 2021-03-06 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.91 Å |
| 7LYB Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c Deposited 2021-03-06 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 7M98 ATAD2 bromodomain complexed with histone H4K5ac (res 1-10) ligand Deposited 2021-03-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
2–16（15 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；2.0 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 6.6
|
Resolution 1.60 Å R-free 0.219 |
| 7NL0 Cryo-EM structure of the Lin28B nucleosome core particle Deposited 2021-02-19 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7PET The 4x177 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 34 PDB declaration: 36-meric（36） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
Chain l
1–103（103 aa）
Chain p
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 9.50 Å |
| 7PEU Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric（27） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.20 Å |
| 7PEV Nucleosome stack of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric（18） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.00 Å |
| 7PEW Nucleosome 1 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 7PEX Nucleosome 2 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.10 Å |
| 7PEY Nucleosome 3 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 7PEZ Nucleosome 4 of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain l
1–103（103 aa）
Chain p
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.90 Å |
| 7PF0 Trinucleosome of the 4x177 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric（28） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 11.00 Å |
| 7PF2 Nucleosome stack of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric（19） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.10 Å |
| 7PF3 Nucleosome 4 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain l
1–103（103 aa）
Chain p
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7PF4 Nucleosome 3 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7PF5 Nucleosome 2 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7PF6 Nucleosome 1 of the 4x187 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7PFA Trinucleosome of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric（28） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 9.70 Å |
| 7PFC Nucleosome stack of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric（19） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.40 Å |
| 7PFD Nucleosome 1 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 7PFE Nucleosome 2 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 7PFF Nucleosome 3 of the 4x197 nucleosome array containing H1 Deposited 2021-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 7PFT Trinucleosome of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 | Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric（29） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 9.80 Å |
| 7PFU Nucleosome stack of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.00 Å |
| 7PFV Nucleosome 1 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 7PFW Nucleosome 2 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.20 Å |
| 7PFX Nucleosome 3 of the 4x207 nucleosome array containing H1 Deposited 2021-08-12 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 7PII Structure of the human CCAN CENP-A alpha-satellite complex Deposited 2021-08-19 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.68 Å |
| 7R5R Structure of the human CCAN CENP-A alpha-satellite complex Deposited 2022-02-11 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.44 Å |
| 7SCY Nuc147 bound to single BRCT Deposited 2021-09-29 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 7SCZ Nuc147 bound to multiple BRCTs Deposited 2021-09-29 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7TAN Structure of VRK1 C-terminal tail bound to nucleosome core particle Deposited 2021-12-21 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.00 Å |
| 7U0G structure of LIN28b nucleosome bound 3 OCT4 Deposited 2022-02-18 | Assembly 1 Insufficient information Heteromer；Protein × 13 PDB declaration: pentadecameric（15） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 7U0I Structure of LIN28b nucleosome bound 2 OCT4 Deposited 2022-02-18 | Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 7U0J Structure of 162bp LIN28b nucleosome Deposited 2022-02-18 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 7U46 Cryo-EM structure of CENP-A nucleosome (palindromic alpha satellite DNA) in complex with CENP-N Deposited 2022-02-28 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.68 Å |
| 7U47 CryoEM structure of CENP-N promoted nucleosome stacks with CENP-A and palindromic alpha satellite DNA sequence Deposited 2022-02-28 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric（22） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain M
1–103（103 aa）
Chain Q
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.50 Å |
| 7U4D CryoEM structure of CENP-N promoted nucleosome stacks with CENP-A and 601 DNA sequence Deposited 2022-02-28 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric（22） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain M
1–103（103 aa）
Chain Q
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.10 Å |
| 7U50 APE1 bound to a nucleosome core particle with AP-site at SHL-6 Deposited 2022-03-01 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7U51 Nucleosome core particle with AP-site at SHL-6 Deposited 2022-03-01 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7U52 nucleosome core particle with AP-site at SHL-6.5 Deposited 2022-03-01 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7U53 Nucleosome core particle with AP-site at SHL0 Deposited 2022-03-01 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7UV9 KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate Deposited 2022-04-29 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 FE FE (III) ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.20 Å |
| 7V1M Structural basis for the co-chaperone relationship of sNASP and ASF1b Deposited 2021-08-04 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；8% v/v Tacsimate, pH 6.0, 20% w/v PEG 3350
|
Resolution 2.83 Å R-free 0.240 |
| 7V1M Structural basis for the co-chaperone relationship of sNASP and ASF1b Deposited 2021-08-04 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain E
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；8% v/v Tacsimate, pH 6.0, 20% w/v PEG 3350
|
Resolution 2.83 Å R-free 0.240 |
| 7V6Q Crystal structure of sNASP-ASF1A-H3.1-H4 complex Deposited 2021-08-20 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
3–103（101 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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain G
3–103（101 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7V96 Telomeric Dinucleosome Deposited 2021-08-24 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric（18） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.92 Å |
| 7V9C Telomeric Dinucleosome in open state Deposited 2021-08-24 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric（18） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 7V9J Telomeric trinucleosome Deposited 2021-08-25 | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
Chain T
1–103（103 aa）
Chain X
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
Chain T
1–103（103 aa）
Chain X
1–103（103 aa）
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.10 Å |
| 7V9S Telomeric trinucleosome in open state Deposited 2021-08-26 | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
Chain T
1–103（103 aa）
Chain X
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 32 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
Chain T
1–103（103 aa）
Chain X
1–103（103 aa）
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 14.00 Å |
| 7VCQ structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 Deposited 2021-09-03 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350
|
Resolution 3.00 Å R-free 0.283 |
| 7VCQ structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 Deposited 2021-09-03 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain E
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350
|
Resolution 3.00 Å R-free 0.283 |
| 7VCQ structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 Deposited 2021-09-03 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain H
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350
|
Resolution 3.00 Å R-free 0.283 |
| 7VZ4 Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA sequence Deposited 2021-11-15 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 1.89 Å |
| 7W9V Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) Deposited 2021-12-10 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.95 Å |
| 7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain b
2–103（102 aa）
Chain f
2–103（102 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain b
2–103（102 aa）
Chain f
2–103（102 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.10 Å |
| 7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain b
2–103（102 aa）
Chain f
2–103（102 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7X57 Cryo-EM structure of human subnucleosome (closed form) Deposited 2022-03-04 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain D
1–103（103 aa）
Chain F
1–103（103 aa）
Chain H
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.63 Å |
| 7X58 Cryo-EM structure of human subnucleosome (open form) Deposited 2022-03-04 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain D
2–103（102 aa）
Chain F
2–103（102 aa）
Chain H
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.93 Å |
| 7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 | Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric（33） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric（35） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 | Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric（33） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric（35） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric（35） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 | Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric（33） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7XVL Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment) Deposited 2022-05-24 | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric（21） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain V
1–103（103 aa）
Chain Z
1–103（103 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 | Assembly 2 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
Chain f
1–103（103 aa）
Chain j
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric（22） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric（21） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric（21） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | 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 | Assembly 2 Protein–DNA Heteromer；Protein × 17 PDB declaration: 21-meric（21） Consistent with all polymers |
Chain V
1–103（103 aa）
Chain Z
1–103（103 aa）
Chain f
1–103（103 aa）
Chain j
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.53 Å |
| 7XZY Cryo-EM structure of the nucleosome containing 193 base-pair DNA with a p53 target sequence Deposited 2022-06-03 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.97 Å |
| 7XZZ Cryo-EM structure of the nucleosome in complex with p53 Deposited 2022-06-03 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.07 Å |
| 7Y00 Cryo-EM structure of the nucleosome containing 169 base-pair DNA with a p53 target sequence Deposited 2022-06-03 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.96 Å |
| 7Y5U Cryo-EM structure of the monomeric human CAF1LC-H3-H4 complex Deposited 2022-06-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain E
1–103（103 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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count |
Chain E
1–103（103 aa）
Chain J
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain D
1–103（103 aa）
Chain F
1–103（103 aa）
Chain H
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain D
1–103（103 aa）
Chain F
1–103（103 aa）
Chain H
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain D
1–103（103 aa）
Chain F
1–103（103 aa）
Chain H
1–103（103 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 | Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 7YOZ Cryo-EM structure of human subnucleosome (intermediate form) Deposited 2022-08-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain D
1–103（103 aa）
Chain F
1–103（103 aa）
Chain H
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 7YWX Structure of the human CCAN CENP-A alpha-satellite complex Deposited 2022-02-14 | Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric（27） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 12.00 Å |
| 7YYH Structure of the human CCANdeltaT CENP-A alpha-satellite complex Deposited 2022-02-17 | Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.90 Å |
| 7ZI4 Cryo-EM structure of the human INO80 complex bound to a WT nucleosome Deposited 2022-04-07 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain J
1–103（103 aa）
Chain N
1–103（103 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 |
| 8AAG H1-bound palindromic nucleosome, state 1 Deposited 2022-07-01 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 10.00 Å |
| 8ATF Nucleosome-bound Ino80 ATPase Deposited 2022-08-23 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain N
2–103（102 aa）
Chain R
2–103（102 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.45 Å |
| 8AV6 CryoEM structure of INO80 core nucleosome complex in closed grappler conformation Deposited 2022-08-26 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain N
2–103（102 aa）
Chain R
2–103（102 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 4.68 Å |
| 8DK5 Structure of 187bp LIN28b nucleosome with site 0 mutation Deposited 2022-07-02 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.71 Å |
| 8EVG 162bp CX3CR1 nucleosome (further classified with better nucleosome end) Deposited 2022-10-20 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.75 Å |
| 8EVH CX3CR1 nucleosome and wild type PU.1 complex Deposited 2022-10-20 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.3
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 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.64 Å |
| 8EVJ CX3CR1 nucleosome bound PU.1 and C/EBPa Deposited 2022-10-20 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8GUI Bre1-nucleosome complex (Model I) Deposited 2022-09-12 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | ZN ZINC ION × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.81 Å |
| 8GUJ Bre1-nucleosome complex (Model II) Deposited 2022-09-12 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | ZN ZINC ION × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8GUK Human nucleosome core particle (free form) Deposited 2022-09-12 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.51 Å |
| 8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 | Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric（24） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 | Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric（24） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 8H1T Cryo-EM structure of BAP1-ASXL1 bound to chromatosome Deposited 2022-10-04 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 | Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric（25） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.95 Å |
| 8HLW Crystal structure of SIRT3 in complex with H4K16la peptide Deposited 2022-12-01 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
14–21（8 aa）
Fragment：residues 20-27, with lactylated No.23 lysine
|
Not recorded | ZN ZINC ION × 1 2OP (2S)-2-HYDROXYPROPANOIC ACID × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；0.1 M Tris pH 8.5, 25% (w/v) Polyethylene glycol 3350
|
Resolution 2.50 Å R-free 0.243 |
| 8IEG Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex Deposited 2023-02-15 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain F
23–102（80 aa）
Chain L
23–102（80 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 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain F
23–102（80 aa）
Chain L
23–102（80 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 | Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric（22） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain N
1–103（103 aa）
Chain R
1–103（103 aa）
Chain V
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.64 Å |
| 8IQF Cryo-EM structure of the dimeric human CAF1-H3-H4 complex Deposited 2023-03-16 | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count |
Chain E
1–103（103 aa）
Chain J
1–103（103 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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain E
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain D
1–103（103 aa）
Chain F
1–103（103 aa）
Chain H
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain D
1–103（103 aa）
Chain F
1–103（103 aa）
Chain H
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 8JCC Human histone H2B variant H2BFWT Cryo-EM structure with 601 DNA sequence Deposited 2023-05-10 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 8JCD Human H2BFWTH100R nucleosome with 601 DNA Deposited 2023-05-11 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.14 Å |
| 8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric（28） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.70 Å |
| 8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8JHF Native SUV420H1 bound to 167-bp nucleosome Deposited 2023-05-23 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
18–103（86 aa）
Chain F
18–103（86 aa）
|
Mutation：K20M Mutation：K20M | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
18–103（86 aa）
Chain F
18–103（86 aa）
|
Mutation：K20M Mutation：K20M | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.65 Å |
| 8JLA Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 Deposited 2023-06-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
17–103（87 aa）
Chain F
17–103（87 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.44 Å |
| 8JLB Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant Deposited 2023-06-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.36 Å |
| 8JLD Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail Deposited 2023-06-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.48 Å |
| 8JND The cryo-EM structure of the nonameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-06-06 | Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: 19-meric（19） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.66 Å |
| 8JNE The cryo-EM structure of the decameric RAD51 ring bound to the nucleosome without the linker DNA binding Deposited 2023-06-06 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric（20） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.68 Å |
| 8JNF The cryo-EM structure of the RAD51 filament bound to the nucleosome Deposited 2023-06-06 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric（16） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.91 Å |
| 8KB5 Cryo-EM structure of the human nucleosome containing H3.8 Deposited 2023-08-03 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.26 Å |
| 8KCY Structure of nucleosome complexed with two DEK molecules Deposited 2023-08-08 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8KD1 Structure of nucleosome complexed with one DEK molecule Deposited 2023-08-08 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8KE0 Structure of H1.2 bound to the nucleosome Deposited 2023-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8OFF Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes (Map1) Deposited 2023-03-15 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric（13） Consistent with all polymers |
Chain Da
1–103（103 aa）
Chain Db
1–103（103 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 |
| 8OL1 cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure) Deposited 2023-03-29 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain B
23–103（81 aa）
Chain F
23–103（81 aa）
|
Not recorded | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4；PBS buffer
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8OO7 CryoEM Structure INO80core Hexasome complex composite model state1 Deposited 2023-04-04 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric（18） Consistent with all polymers |
Chain N
2–103（102 aa）
Chain R
2–103（102 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 | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric（8） Consistent with all polymers |
Chain N
2–103（102 aa）
Chain R
2–103（102 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 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric（18） Consistent with all polymers |
Chain N
2–103（102 aa）
Chain R
2–103（102 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 | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric（9） Consistent with all polymers |
Chain N
2–103（102 aa）
Chain R
2–103（102 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.2
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 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.90 Å |
| 8OTS OCT4 and MYC-MAX co-bound to a nucleosome Deposited 2023-04-21 | Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
22–103（82 aa）
Chain F
22–103（82 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8；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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8；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 |
| 8PEF Crystal structure of SLF1 Ankyrin repeat domain in complex with H4 tail (K20me0) Deposited 2023-06-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
10–26（17 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1M Sodium malonate dibasic monohydrate
0.1M Hepes pH 7
30% (w/v) Poly(acrylic acid sodium salt) 2100
|
Resolution 1.28 Å R-free 0.225 |
| 8Q36 Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound) Deposited 2023-08-03 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain BBB
17–103（87 aa）
Chain FFF
17–103（87 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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain BBB
17–103（87 aa）
Chain FFF
17–103（87 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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain BBB
17–103（87 aa）
Chain FFF
17–103（87 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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain BBB
17–103（87 aa）
Chain FFF
17–103（87 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 |
| 8QZM Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome Deposited 2023-10-27 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；15 mM HEPES pH 7.5, 65 mM NaCl, 1 mM DTT, 0.1 mM S-Adenosyl methionine
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8RBX Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex Deposited 2023-12-05 | Assembly 1 Other combination Heteromer；Protein × 43 PDB declaration: 46-meric（46） Consistent with all polymers |
Chain O
1–103（103 aa）
Chain U
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8RGM Cryo-EM structure of nucleosome containing Widom603 DNA Deposited 2023-12-14 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8SB6 Structure of human BRD2-BD1 bound to a histone H4 acetyl-methyllysine peptide Deposited 2023-04-02 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
2–16（15 aa）
Fragment：N-terminal 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, SITTING DROP；293 K；0.1 M MES, pH 6.7, 20-25% PEG5000 MME, 0.2 M ammonium sulfate
|
Resolution 1.80 Å R-free 0.204 |
| 8SB6 Structure of human BRD2-BD1 bound to a histone H4 acetyl-methyllysine peptide Deposited 2023-04-02 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
2–16（15 aa）
Fragment：N-terminal 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, SITTING DROP；293 K；0.1 M MES, pH 6.7, 20-25% PEG5000 MME, 0.2 M ammonium sulfate
|
Resolution 1.80 Å R-free 0.204 |
| 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8SPU Structure of ESRRB nucleosome bound OCT4 at site c Deposited 2023-05-03 | Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8SYP Genomic CX3CR1 nucleosome Deposited 2023-05-25 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 8TGP Crystal structure of SIRT2 with FAM-PEG4-H4K16(myristoyl) peptide Deposited 2023-07-12 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
9–21（13 aa）
|
Not recorded | ZN ZINC ION × 1 MYR MYRISTIC ACID × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M MES monohydrate pH 6.5 (NaOH), 20% w/v PEG 4,000
|
Resolution 1.76 Å R-free 0.230 |
| 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 8UBJ Cryo-EM structure of NRCAM nucleosome aided by scFv (3D Flex map) Deposited 2023-09-23 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8UBK Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome Deposited 2023-09-23 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 8UBL Cryo-EM structure of Ascl1/E12a in complex with NRCAM nucleosome (3D Flex map) Deposited 2023-09-23 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8UPF Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c Deposited 2023-10-22 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.65 Å |
| 8VFY Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 1) Deposited 2023-12-22 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.89 Å |
| 8VFZ Cryo-EM structure of FoxA1 in complex with ALBN1 nucleosome (class 2) Deposited 2023-12-22 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8VG0 Cryo-EM structure of GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.07 Å |
| 8VG1 Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome Deposited 2023-12-22 | Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.48 Å |
| 8VG2 Cryo-EM structure of FoxA1 and GATA4 in complex with H14 chromatosome Deposited 2023-12-22 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 8VLR Cryo-EM structure of native H2AK119bu nucleosome at 2.6 Deposited 2024-01-12 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
20–103（84 aa）
Chain F
20–103（84 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 |
| 8VMJ H3K4me3 nucleosome bound to PRC2_AJ119-450 Deposited 2024-01-13 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain J
1–103（103 aa）
Chain Q
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8VMN H3K4me3 nucleosome bound to PRC2_AJ1-450 Deposited 2024-01-13 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain J
1–103（103 aa）
Chain Q
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8VO0 H3K36me3-modified nucleosome bound to PRC2_AJ1-450 with histone H3 tail disengaged Deposited 2024-01-14 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain J
26–103（78 aa）
Chain Q
25–103（79 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8VOB H3K36me3-modified nucleosome bound to PRC2_AJ1-450 Deposited 2024-01-14 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain J
1–103（103 aa）
Chain Q
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8VWS Nucleosome containing 8oxoG at SHL-6 Deposited 2024-02-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and
1 mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8VWT OGG1 bound to a nucleosome containing 8oxoG at SHL-6 (composite map) Deposited 2024-02-02 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and
1 mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8VWU Nucleosome containing 8oxoG at SHL4 Deposited 2024-02-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and
1 mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8VWV OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map) Deposited 2024-02-02 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；50 mM HEPES (pH-7.1), 100 mM NaCl, 1 mM TCEP, and
1 mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8W9D Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1 Deposited 2023-09-05 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric（18） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric（17） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric（17） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
24–102（79 aa）
Chain F
24–102（79 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 | Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric（25） Consistent with all polymers |
Chain D
1–103（103 aa）
Chain H
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric（25） Consistent with all polymers |
Chain D
1–103（103 aa）
Chain H
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric（25） Consistent with all polymers |
Chain D
1–103（103 aa）
Chain H
1–103（103 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 |
| 8X7I Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Deposited 2023-11-24 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
20–102（83 aa）
Chain F
20–102（83 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.27 Å |
| 8X7J Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Deposited 2023-11-24 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
21–102（82 aa）
Chain F
21–102（82 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.39 Å |
| 8X7K Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination) Deposited 2023-11-24 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
21–102（82 aa）
Chain F
21–102（82 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.27 Å |
| 8XBT The cryo-EM structure of the octameric RAD51 ring bound to the nucleosome with the linker DNA binding Deposited 2023-12-07 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric（18） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 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 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric（20） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.89 Å |
| 8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain b
2–103（102 aa）
Chain f
2–103（102 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 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain b
2–103（102 aa）
Chain f
2–103（102 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 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.21 Å |
| 8Y3D Cryo-EM structure of the overlapping di-nucleosome (intermediate form2) Deposited 2024-01-29 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.10 Å |
| 8Y3E Cryo-EM structure of the overlapping di-nucleosome (open form) Deposited 2024-01-29 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric（16） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.32 Å |
| 8Y3F Cryo-EM structure of the overlapping di-nucleosome (intermediate form1) Deposited 2024-01-29 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric（16） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.54 Å |
| 8YBJ Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence Deposited 2024-02-14 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.38 Å |
| 8YBK Cryo-EM structure of the human nucleosome containing the H3.1 E97K mutant Deposited 2024-02-14 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.69 Å |
| 8YE8 Crystal structure of mouse BAHCC1 TTD domain in complex with H4K20me1 peptide Deposited 2024-02-22 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
15–26（12 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；293 K；100 mM MES, pH 6.5, 10 mM Li2SO4, 8% PEG20000 and 3 mM H4K20me
|
Resolution 1.90 Å R-free 0.238 |
| 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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count |
Chain D
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, 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 | Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric（7） Consistent with protein count |
Chain D
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, 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 | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: 13-meric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.52 Å |
| 8YTI Crystal Structure of Nucleosome-H1x Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2024-03-26 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric（22） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain L
1–103（103 aa）
Chain P
1–103（103 aa）
|
Not recorded | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 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 |
| 8Z50 Crystal structure of the ASF1-H3T-H4 complex Deposited 2024-04-18 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；1.0 M Lithium chloride, 0.1 M MES pH 6.0, 10% PEG 6000
|
Resolution 2.80 Å R-free 0.255 |
| 8ZJR Structure of nucleosome-bound RFX5 complex Deposited 2024-05-15 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8ZJT Structure of free nucleosome Deposited 2024-05-15 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9BE6 Cryo-EM structure of Human Nucleosome collected by Leginon on Krios at 3.0 Angstrom resolution Deposited 2024-04-14 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain F
26–103（78 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9D3K Two Dsup molecules in complex with the nucleosome open from both sides Deposited 2024-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
24–102（79 aa）
Chain F
24–102（79 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 9D3L Two Dsup molecules in complex with the nucleosome open from the left side Deposited 2024-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
24–102（79 aa）
Chain F
24–102（79 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9D3M Two HMGN2s in complex with the nucleosome Deposited 2024-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
22–103（82 aa）
Chain F
22–103（82 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9D3N 167-bp 5S rDNA nucleosome cross-linked with glutaraldehyde Deposited 2024-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
25–103（79 aa）
Chain F
25–103（79 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9D3O 167-bp 5S rDNA nucleosome - closed Deposited 2024-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
22–103（82 aa）
Chain F
22–103（82 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9D3P 167-bp 5S rDNA nucleosome - open I (open only on the downstream side) Deposited 2024-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
22–103（82 aa）
Chain F
22–103（82 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 9D3Q 167-bp 5S rDNA nucleosome - open II Deposited 2024-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
23–103（81 aa）
Chain F
23–103（81 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9D3R 147-bp 5S rDNA nucleosome - closed Deposited 2024-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
22–103（82 aa）
Chain F
22–103（82 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9D3S 147-bp 5S rDNA nucleosome - open I (open on the downstream side) Deposited 2024-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
22–103（82 aa）
Chain F
22–103（82 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9D3T 147-bp 5S rDNA nucleosome cross-linked with glutaraldehyde Deposited 2024-08-11 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
25–102（78 aa）
Chain F
25–102（78 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9DWF Nucleosome containing a 1-nt gap at SHL-4.5 Deposited 2024-10-09 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and
5mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9DWG DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 1, composite) Deposited 2024-10-09 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and
5mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9DWH DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 2, composite) Deposited 2024-10-09 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and
5mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9DWI DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 3, composite) Deposited 2024-10-09 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and
5mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9DWJ Nucleosome containing a 1-nt gap at SHL-3.5 Deposited 2024-10-09 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and
5mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9DWK DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-3.5 Deposited 2024-10-09 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and
5mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 9DWL Nucleosome containing a 1-nt gap at SHL-5.5 Deposited 2024-10-09 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；25mM HEPES (pH-7.1), 50mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 9DWM DNA polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5 Deposited 2024-10-09 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；25mM HEPES (pH-7.1), 50mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 9E00 Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain N
1–103（103 aa）
Chain R
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.75 Å |
| 9E05 The consensus model of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain N
1–103（103 aa）
Chain R
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.00 Å |
| 9E09 Cryo-EM structure a single nucleosome (2) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-17 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain N
1–103（103 aa）
Chain R
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.72 Å |
| 9E0R Cryo-EM structure of a single nucleosome (1) focus of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome Deposited 2024-10-18 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9E2D Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome with a five base pair linker Deposited 2024-10-22 | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain N
1–103（103 aa）
Chain R
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.08 Å |
| 9E2F Cryo-EM structure of a di-nucleosome with a five base pair linker Deposited 2024-10-22 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric（18） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain N
1–103（103 aa）
Chain R
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.90 Å |
| 9E2Q Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with a six base pair linker Deposited 2024-10-22 | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain N
1–103（103 aa）
Chain R
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.14 Å |
| 9E2R Cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to a di-nucleosome and an histone-3 peptide Deposited 2024-10-22 | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain N
1–103（103 aa）
Chain R
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.71 Å |
| 9E3D Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with K120R mutant H2B Deposited 2024-10-23 | Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric（22） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain N
1–103（103 aa）
Chain R
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 9E3R Cryo-EM structure of PWWP domain deleted DNMT 3A2/3B3 in complex with a di-nucleosome Deposited 2024-10-23 | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain N
1–103（103 aa）
Chain R
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.90 Å |
| 9E3U Cryo-EM structure of DNMT 3A2/3B3 tetramer bound to a di-nucleosome with a 25 base-pair linker Deposited 2024-10-24 | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric（15） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 9 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.90 Å |
| 9E49 Cryo-EM structure of a di-nucleosome with an eight base-pair linker Deposited 2024-10-24 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric（18） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain N
1–103（103 aa）
Chain R
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.93 Å |
| 9ECP Structure of the native human NCP purified from HEK293 cells Deposited 2024-11-14 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
22–103（82 aa）
Chain F
22–103（82 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 |
| 9EOZ Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0 Deposited 2024-03-16 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9FGQ Structure of human APC3loop 375-381 bound to the NCP Deposited 2024-05-24 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8；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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 9GCG CryoEM structure of the human INO80 core- H2A.Z nucleosome complex Deposited 2024-08-01 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric（20） Consistent with all polymers |
Chain N
2–103（102 aa）
Chain R
2–103（102 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain N
2–103（102 aa）
Chain R
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.52 Å |
| 9GE5 CryoEM structure of the human INO80-Hexasome complex Deposited 2024-08-07 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric（18） Consistent with all polymers |
Chain N
23–103（81 aa）
Chain R
26–103（78 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 | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric（8） Consistent with all polymers |
Chain N
2–103（102 aa）
Chain R
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.86 Å |
| 9GEV CryoEM structure of the human INO80 core-nucleosome complex state N-6 Deposited 2024-08-07 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric（20） Consistent with all polymers |
Chain N
2–103（102 aa）
Chain R
2–103（102 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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain N
2–103（102 aa）
Chain R
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 9GFB CryoEM structure of the human INO80 core-nucleosome complex state N-7 Deposited 2024-08-08 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric（20） Consistent with all polymers |
Chain N
2–103（102 aa）
Chain R
2–103（102 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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain N
22–103（82 aa）
Chain R
25–103（79 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 |
| 9GMK SIRT7:H3K18DTU nucleosome complex Deposited 2024-08-29 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9GMR SIRT7-H3K36MTUnucleosome complex Deposited 2024-08-29 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | A1IY0 [[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-2-(methylamino)-6-oxidanyl-2-(propylamino)-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9GW2 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Deposited 2024-09-26 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.84 Å |
| 9GXA CENP-A/H4 di-tetrasome assembled on alpha-satellite DNA. Deposited 2024-09-29 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain D
2–103（102 aa）
Chain F
2–103（102 aa）
Chain H
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.01 Å |
| 9IGW Ku70/80 bound to 147 bp nucleosome Deposited 2025-02-20 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 9IGX Ku70/80 bound to 153 bp nucleosome Deposited 2025-02-20 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
Chain B
18–101（84 aa）
Chain F
18–101（84 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 |
| 9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 | Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric（24） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9IPU cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Deposited 2024-07-11 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 9J0N Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc) Deposited 2024-08-02 | Assembly 1 Other combination Heteromer；Protein × 27 PDB declaration: 30-meric（30） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9J0O Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc) Deposited 2024-08-02 | Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric（29） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9J0P Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc) Deposited 2024-08-02 | Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric（29） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9J8M Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (High mobility complex) Deposited 2024-08-21 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.82 Å |
| 9J8N Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (Low mobility complex) Deposited 2024-08-21 | Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 32-meric（32） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.14 Å |
| 9J8O Cryo-EM structure of BAF-Lamin A/C IgF-H1-nucleosome complex Deposited 2024-08-21 | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 28-meric（28） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.05 Å |
| 9J8W Cryo-EM structure of NCP-UV-DDB complex containing CPD Deposited 2024-08-21 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.38 Å |
| 9JC6 Human H2BW2 nucleosome Deposited 2024-08-28 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.34 Å |
| 9K9L Cryo-EM structure of the human CENP-A-H4 octasome. Deposited 2024-10-27 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain D
1–103（103 aa）
Chain F
1–103（103 aa）
Chain H
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.66 Å |
| 9KQO cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome Deposited 2024-11-26 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain F
2–103（102 aa）
Chain L
2–103（102 aa）
|
Not recorded | ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.48 Å |
| 9L1X hDEK-nucleosome complex (conformation 1) Deposited 2024-12-16 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | UNX UNKNOWN LIGAND × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.69 Å |
| 9L22 hDEK-nucleosome complex (conformation 2) Deposited 2024-12-16 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | UNX UNKNOWN LIGAND × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9MLL GammaH2AX containing nucleosomes, Parallel stack Deposited 2024-12-19 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain M
1–103（103 aa）
Chain Q
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 9MLN GammaH2AX containing nucleosome, Canonical (Class 1) Deposited 2024-12-19 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9MLR GammaH2AX containing nucleosome, Half-wrapped (Class 2) Deposited 2024-12-19 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9MLS GammaH2AX containing nucleosome, Extended (Class 3) Deposited 2024-12-19 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 9MMK H2AX containing nucleosome, Canonical (Class 1) Deposited 2024-12-20 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9MMM H2AX containing nucleosomes, Parallel stack Deposited 2024-12-20 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain M
1–103（103 aa）
Chain Q
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain M
1–103（103 aa）
Chain Q
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain M
1–103（103 aa）
Chain Q
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9NQU KDM6B-nucleosome structure stabilized by H3K27C-UNC8015 covalent conjugate Deposited 2025-03-13 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | FE FE (III) ION × 1 ZN ZINC ION × 1 OH0 N-heptanoyl-N-hydroxy-beta-alanine × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.16 Å |
| 9OGR Cryo-EM analysis of human H2A.Z on methylated Sat2R-P DNA (v1) Deposited 2025-05-01 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.78 Å |
| 9OGS Cryo-EM analysis of human H2A.Z on Sat2R-P DNA (v1) Deposited 2025-05-01 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.05 Å |
| 9OGZ Cryo-EM analysis of human H2A.Z on Sat2R-P DNA (v2) Deposited 2025-05-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.05 Å |
| 9OH0 Cryo-EM analysis of human H2A.Z on methylated Sat2R-P DNA (v2) Deposited 2025-05-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.78 Å |
| 9OH1 Cryo-EM analysis of human H2A.Z on 601L DNA Deposited 2025-05-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.09 Å |
| 9OH2 Cryo-EM analysis of human H2A.Z on methylated 601L DNA Deposited 2025-05-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.14 Å |
| 9Q80 Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome Deposited 2025-02-21 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.39 Å |
| 9Q8X Ku70/80 bound to a 153 bp H2AX nucleosome Deposited 2025-02-25 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
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 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
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 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric（13） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
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 | Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.38 Å |
| 9QMS DNA-PK bound to 153 bp H2AX nucleosome with ATPyS Deposited 2025-03-24 | Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 30-meric（30） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.00 Å |
| 9R04 p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample) Deposited 2025-04-24 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 9R2M p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, composite map) Deposited 2025-04-30 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9R2P p53 bound to nucleosome at position SHL+5.9 (crosslinked sample) Deposited 2025-04-30 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.18 Å |
| 9R2Q p53 bound to nucleosome at position SHL-5.7 (non-crosslinked sample) Deposited 2025-04-30 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9RL4 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6 Deposited 2025-06-16 | Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric（22） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 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 | Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric（22） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 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 | Assembly 1 Insufficient information Heteromer；Protein × 20 PDB declaration: 22-meric（22） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.90 Å |
| 9RN2 Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2 Deposited 2025-06-19 | Assembly 1 Insufficient information Heteromer；Protein × 19 PDB declaration: 21-meric（21） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 9RZC State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Deposited 2025-07-15 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.66 Å |
| 9RZE State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Deposited 2025-07-15 | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.53 Å |
| 9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17 | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric（35） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.72 Å |
| 9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24 | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.40 Å |
| 9TAX Structure of the human inner kinetochore CCAN bound to a mono-CENP-A nucleosome Deposited 2025-11-18 | Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric（27） Consistent with all polymers |
Chain d
1–103（103 aa）
Chain h
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 9TAY Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome Deposited 2025-11-18 | Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 37-meric（37） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain d
1–103（103 aa）
Chain h
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 15.50 Å |
| 9U5U The 1:1 cryo-EM structure of BAP1/ASXL1-K351Ub in complex with H2AK119Ub nucleosome Deposited 2025-03-21 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.12 Å |
| 9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain d
1–103（103 aa）
Chain f
1–103（103 aa）
Chain h
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.62 Å |
| 9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 | Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric（19） Consistent with all polymers |
Chain f
1–103（103 aa）
Chain h
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.54 Å |
| 9UZ7 Cryo-EM structure of the nucleosome core particle with site-specific DNA-histone crosslinking Deposited 2025-05-16 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain C
2–103（102 aa）
Chain D
2–103（102 aa）
|
Not recorded | 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 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.00 Å |
| 9V6X Cryo-EM structure of the cPRC1 complex bound to an endogenous 184-bp mono-nucleosome Deposited 2025-05-27 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 4.00 Å |
| 9V8L Cryo-EM structure of the cPRC1-di-nucleosome (loose) complex Deposited 2025-05-29 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric（20） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain S
1–103（103 aa）
Chain T
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric（22） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain Q
1–103（103 aa）
Chain R
1–103（103 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 | Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric（24） Consistent with all polymers |
Chain B
1–103（103 aa）
Chain F
1–103（103 aa）
Chain Q
1–103（103 aa）
Chain R
1–103（103 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.40 Å |
| 9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.59 Å |
| 9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.28 Å |
| 9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.66 Å |
| 9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain b
1–103（103 aa）
Chain f
1–103（103 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.62 Å |
| 9XSF Cryo-EM structure of H4S47GlcNAc nucleosome at 3.39 angstrom Deposited 2025-11-20 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.39 Å |
| 9Y46 Human nucleosome structure on Nickel-NTA lipid affinity grid (C2 refinement) Deposited 2025-09-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.59 Å |
| 9Y47 Human nucleosome structure on Nickel-NTA lipid affinity grid (C1 refinement) Deposited 2025-09-02 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.74 Å |
| 9YL3 State 1 MLL4FC bound to a nucleosome premodified with H2BK120ub and H4K16ac Deposited 2025-10-08 | Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric（17） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 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 | Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: 17-meric（17） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 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 | Assembly 1 Insufficient information Heteromer；Protein × 14 PDB declaration: 16-meric（16） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 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 | Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric（18） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | 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 | Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: 18-meric（18） Consistent with all polymers |
Chain B
2–103（102 aa）
Chain F
2–103（102 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.45 Å |
| 9ZEN Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2 Deposited 2025-11-30 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
Chain B
25–103（79 aa）
Chain F
25–103（79 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.17 Å |
| 9ZEO Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1 Deposited 2025-11-30 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain B
21–103（83 aa）
Chain F
21–103（83 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.6；20 mM HEPES pH7.6, 50 mM NaCl, 0.5 mM MgCl2, 1 mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
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Resolution 3.10 Å |