Histone H3
Xenopus laevis
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein–DNA Heteromer Protein × 24 DNA 2 PDB declaration: 26-meric（26） Consistent with all polymer counts | Chain A； UniProt 2–136 | Non-standard monomer：Yes (specific site not provided by mmCIF) | Histone H4 × 4 （P62799） Histone H2A type 1 × 4 （P06897） Histone H2B 1.1 × 4 （P02281） Histone H3.2 × 3 （P84233） DNA (321-MER) × 1 DNA (321-MER) × 1 Isoform 7 of DNA (cytosine-5)-methyltransferase 3B × 4 （Q9UBC3） DNA (cytosine-5)-methyltransferase 3A × 4 （Q9Y6K1） ZN ZINC ION × 18 SAH S-ADENOSYL-L-HOMOCYSTEINE × 4 | ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE | Resolution 3.84 Å |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 9Y4P | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1S32 Molecular Recognition of the Nucleosomal 'Supergroove' Deposited 2004-01-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MN MANGANESE (II) ION × 14 IMT 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID × 4 PYB 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID × 12 ABU GAMMA-AMINO-BUTANOIC ACID × 2 BAL BETA-ALANINE × 2 DIB 3-AMINO-(DIMETHYLPROPYLAMINE) × 2 OGG 2-(2-CARBAMOYLMETHOXY-ETHOXY)-ACETAMIDE × 1 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；Manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
|
Resolution 2.05 Å R-free 0.243 |
| 21VV Cryo-EM structure of ncBAF bound to the nucleosome Deposited 2025-12-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；20 mM HEPES pH 8.0, 100 mM KCl, 2 mM MgCl2, 2 mM DTT, 0.5 mM ADP, 8 mM NaF, 1 mM BeSO4.
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.70 Å |
| 21WA Cryo-EM structure of the ATPase domain of SMARCA4 bound to a nucleosome Deposited 2025-12-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；20 mM HEPES pH 8.0, 100 mM KCl, 2 mM MgCl2, 2 mM DTT, 0.5 mM ADP, 8 mM NaF, 1 mM BeSO4.
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 21WC Cryo-EM structure of the ATPase domain of SMARCA4 and the finger helix of BCL7A bound to a nucleosome Deposited 2025-12-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；20 mM HEPES pH 8.0, 100 mM KCl, 2 mM MgCl2, 2 mM DTT, 0.5 mM ADP, 8 mM NaF, 1 mM BeSO4.
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 6IRO the crosslinked complex of ISWI-nucleosome in the ADP-bound state Deposited 2018-11-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 6IY2 Structure of Snf2-MMTV-A nucleosome complex at shl2 in ADP state Deposited 2018-12-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
37–136（100 aa）
Chain E
37–136（100 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.47 Å |
| 6IY3 Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state Deposited 2018-12-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
37–136（100 aa）
Chain E
37–136（100 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.67 Å |
| 6J99 Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome Deposited 2019-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 6JYL The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state Deposited 2019-04-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot 1.5s
|
Resolution 3.37 Å |
| 6K1P The complex of ISWI-nucleosome in the ADP.BeF-bound state Deposited 2019-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5；10 mM Tris, 50 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 1.5s
|
Resolution 3.87 Å |
| 6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 6KIW Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 6KIX Cryo-EM structure of human MLL1-NCP complex, binding mode1 Deposited 2019-07-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 6KIZ Cryo-EM structure of human MLL1-NCP complex, binding mode2 Deposited 2019-07-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 6NZO Set2 bound to nucleosome Deposited 2019-02-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K36M Mutation：K36M | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 6PX1 Set2 bound to nucleosome Deposited 2019-07-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K36M Mutation：K36M | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 6PX3 Set2 bound to nucleosome Deposited 2019-07-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K36M Mutation：K36M | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 6R1T Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 1, free nuclesome Deposited 2019-03-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
38–136（99 aa）
Chain E
38–136（99 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.02 Å |
| 6R1U Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2 Deposited 2019-03-15 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain M
2–136（135 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.36 Å |
| 6R25 Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3 Deposited 2019-03-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
Chain M
2–136（135 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.61 Å |
| 6S01 Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome Deposited 2019-06-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 4 seconds before plunging
|
Resolution 3.20 Å |
| 6VYP Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate Deposited 2020-02-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：K4M Mutation：K4M | FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 7.5；277 K；25 mM HEPES pH7.5,
75 mM triammonium citrate,
10% PEG2000-MME,
Modified Microbatch under oil
|
Resolution 4.99 Å R-free 0.277 |
| 6VYP Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate Deposited 2020-02-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain a
2–136（135 aa）
Chain e
2–136（135 aa）
|
Mutation：K4M Mutation：K4M | FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 7.5；277 K；25 mM HEPES pH7.5,
75 mM triammonium citrate,
10% PEG2000-MME,
Modified Microbatch under oil
|
Resolution 4.99 Å R-free 0.277 |
| 6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain C
39–136（98 aa）
Chain H
39–136（98 aa）
|
Not recorded | GOL GLYCEROL × 3 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
|
Resolution 2.35 Å R-free 0.233 |
| 6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain M
39–136（98 aa）
Chain R
39–136（98 aa）
|
Not recorded | GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
|
Resolution 2.35 Å R-free 0.233 |
| 6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain W
39–136（98 aa）
Chain b
39–136（98 aa）
|
Not recorded | GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
|
Resolution 2.35 Å R-free 0.233 |
| 6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain g
39–136（98 aa）
Chain l
39–136（98 aa）
|
Not recorded | GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
|
Resolution 2.35 Å R-free 0.233 |
| 6Z6P HDAC-PC-Nuc Deposited 2020-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
39–135（97 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.43 Å |
| 6ZHX Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: nucleosome class. Deposited 2020-06-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：C110A Mutation：C110A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Blot time 2.5 s, blot force 0.
Two sample applications and blots were performed before vitrification.
|
Resolution 2.50 Å |
| 6ZHY Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: hexasome class. Deposited 2020-06-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：C110A Mutation：C110A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Blot time 2.5 s, blot force 0.
Two sample applications and blots were performed before vitrification.
|
Resolution 3.00 Å |
| 7E8I Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7EA5 Yeast Set2 bound to a nucleosome containing oncohistone mutations Deposited 2021-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
35–135（101 aa）
Chain E
35–135（101 aa）
|
Mutation：K37M Mutation：K37M | ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7KTQ Nucleosome from a dimeric PRC2 bound to a nucleosome Deposited 2020-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
38–136（99 aa）
Chain E
38–136（99 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7M1X Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z Deposited 2021-03-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 4.5 seconds before plunging
|
Resolution 3.70 Å |
| 7MBM Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 Deposited 2021-04-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain G
1–136（136 aa）
Chain K
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.76 Å |
| 7MBN Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02 Deposited 2021-04-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain G
1–136（136 aa）
Chain K
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.02 Å |
| 7SWY 2.6 A structure of a 40-601[TA-rich+1]-40 nucleosome Deposited 2021-11-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：C110A Mutation：C110A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；20 mM HEPES, pH 7.0, 60 mM KCl, 1.5 mM DTT, 1 mM MgCl2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 7TN2 Composite model of a Chd1-nucleosome complex in the nucleotide-free state derived from 2.3A and 2.7A Cryo-EM maps Deposited 2022-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：C110A Mutation：C110A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；20 mM HEPES, pH 7.0, 60 mM KCl, 1.5 mM DTT, 1 mM MgCl2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K4Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K4Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.25 Å |
| 7VDT The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex Deposited 2021-09-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain E
1–136（136 aa）
Chain K
1–136（136 aa）
|
Not recorded | BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7VDV The overall structure of human chromatin remodeling PBAF-nucleosome complex Deposited 2021-09-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric |
Chain E
1–136（136 aa）
Chain K
1–136（136 aa）
|
Not recorded | BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7VVU NuA4 HAT module bound to the nucleosome Deposited 2021-11-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric |
Chain A
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | CMC CARBOXYMETHYL COENZYME *A × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 3.40 Å |
| 7VVZ NuA4 bound to the nucleosome Deposited 2021-11-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric |
Chain A
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | CMC CARBOXYMETHYL COENZYME *A × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 8.80 Å |
| 7X3T Cryo-EM structure of ISW1a-dinucleosome Deposited 2022-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
Chain K
1–136（136 aa）
Chain O
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.40 Å |
| 7X3V Cryo-EM structure of IOC3-N2 nucleosome Deposited 2022-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.09 Å |
| 7X3W Cryo-EM structure of ISW1-N1 nucleosome Deposited 2022-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7X3X Cryo-EM structure of N1 nucleosome-RA Deposited 2022-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
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 |
| 7XPX Cryo-EM structure of the histone methyltransferase SET8 bound to H4K20Ecx-nucleosome Deposited 2022-05-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7YI1 Cryo-EM structure of Eaf3 CHD bound to H3K36me3 nucleosome Deposited 2022-07-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7YI4 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in close state Deposited 2022-07-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
Chain G
2–136（135 aa）
Chain K
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.96 Å |
| 7YI5 Cryo-EM structure of Rpd3S complex bound to H3K36me3 nucleosome in loose state Deposited 2022-07-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
Chain G
2–136（135 aa）
Chain K
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.96 Å |
| 8B0A Cryo-EM structure of ALC1 bound to an asymmetric, site-specifically PARylated nucleosome Deposited 2022-09-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8CBN structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Deposited 2023-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.34 Å |
| 8CBQ structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Deposited 2023-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8DU4 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Deposited 2022-07-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K4Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K4Nle, M90Nle, M120Nle Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.55 Å |
| 8ETT Class1 of the INO80-Hexasome complex Deposited 2022-10-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 6.68 Å |
| 8ETV Class2 of the INO80-Hexasome complex Deposited 2022-10-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 3.16 Å |
| 8EU2 Class3 of the INO80-Hexasome complex Deposited 2022-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 2.93 Å |
| 8EUE Class1 of the INO80-Nucleosome complex Deposited 2022-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 3.48 Å |
| 8EUJ Class2 of the INO80-Nucleosome complex Deposited 2022-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 3.36 Å |
| 8G57 Structure of nucleosome-bound Sirtuin 6 deacetylase Deposited 2023-02-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
4–135（132 aa）
Chain E
4–135（132 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；12.5 mM HEPES pH 7.5, 60 mM KCl, 1.5% glycerol, 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.07 Å |
| 8G6G H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 5 Deposited 2023-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K79(MLY), C110A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K79(MLY), C110A Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.93 Å |
| 8G6H H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 6 Deposited 2023-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K79(MLY), C110A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K79(MLY), C110A Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.06 Å |
| 8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric |
Chain NA
1–136（136 aa）
Chain NE
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.04 Å |
| 8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric |
Chain NA
1–136（136 aa）
Chain NE
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.16 Å |
| 8HXX Cryo-EM structure of the histone deacetylase complex Rpd3S Deposited 2023-01-05 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain E
2–136（135 aa）
|
Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8HXY Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Deposited 2023-01-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8HXZ Cryo-EM structure of Eaf3 CHD in complex with nucleosome Deposited 2023-01-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8HY0 Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Deposited 2023-01-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8IHM Eaf3 CHD domain bound to the nucleosome Deposited 2023-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.58 Å |
| 8IHN Cryo-EM structure of the Rpd3S core complex Deposited 2023-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
2–25（24 aa）
Fragment：N-ter
|
Not recorded | ZN ZINC ION × 1 CA CALCIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.37 Å |
| 8IHT Rpd3S bound to the nucleosome Deposited 2023-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 CA CALCIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.72 Å |
| 8JHO Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome Deposited 2023-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
Chain a
2–136（135 aa）
Chain e
2–136（135 aa）
|
Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.60 Å |
| 8KD2 Rpd3S in complex with 187bp nucleosome Deposited 2023-08-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
Chain O
2–136（135 aa）
Chain S
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.02 Å |
| 8KD3 Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA Deposited 2023-08-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
Chain O
2–136（135 aa）
Chain S
2–136（135 aa）
|
Mutation：C110A, K9Q Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C110A, K9Q Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8KD4 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1 Deposited 2023-08-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
Chain O
2–136（135 aa）
Chain S
2–136（135 aa）
|
Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.93 Å |
| 8KD5 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2 Deposited 2023-08-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric |
Chain O
2–136（135 aa）
Chain S
2–136（135 aa）
|
Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8KD6 Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3 Deposited 2023-08-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
Chain O
2–136（135 aa）
Chain S
2–136（135 aa）
|
Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.07 Å |
| 8KD7 Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA Deposited 2023-08-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: hexadecameric |
Chain O
2–136（135 aa）
Chain S
2–136（135 aa）
|
Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C110A Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.09 Å |
| 8PC5 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex Deposited 2023-06-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.02 Å |
| 8PC6 H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Deposited 2023-06-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 8PEO H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex Deposited 2023-06-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.69 Å |
| 8PEP H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Deposited 2023-06-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric |
Chain A
2–136（135 aa）
Chain E
39–136（98 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.33 Å |
| 8RUP Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome Deposited 2024-01-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric |
Chain E
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blotting time, -10 force, no wait time.
|
Resolution 2.42 Å |
| 8RUQ Borealin N-terminus in complex with H3.T3p-nucleosome Deposited 2024-01-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain E
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；10 mM TRIS-HCl, pH 7.5, 150 mM NaCl, 2 mM DTT, 0.3% n-octyl-beta-D-glucoside
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blotting time, -10 force, no wait time.
|
Resolution 2.29 Å |
| 8TOF Rpd3S bound to an H3K36Cme3 modified nucleosome Deposited 2023-08-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: octadecameric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8XJV Structural basis for the linker histone H5-nucleosome binding and chromatin compaction Deposited 2023-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 108 PDB declaration: 110-meric |
Chain X
1–136（136 aa）
Chain Y
1–136（136 aa）
Chain Z
1–136（136 aa）
Chain a
1–136（136 aa）
Chain b
1–136（136 aa）
Chain c
1–136（136 aa）
Chain d
1–136（136 aa）
Chain e
1–136（136 aa）
Chain f
1–136（136 aa）
Chain g
1–136（136 aa）
Chain h
1–136（136 aa）
Chain i
1–136（136 aa）
Chain j
1–136（136 aa）
Chain k
1–136（136 aa）
Chain l
1–136（136 aa）
Chain m
1–136（136 aa）
Chain n
1–136（136 aa）
Chain o
1–136（136 aa）
Chain p
1–136（136 aa）
Chain q
1–136（136 aa）
Chain r
1–136（136 aa）
Chain s
1–136（136 aa）
Chain t
1–136（136 aa）
Chain u
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 3.60 Å |
| 9C9X S.c INO80 in complex with Xenopus 0/80 nucleosome, Nucleosome Deposited 2024-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 2.83 Å |
| 9CAN S.c INO80 in complex with Xenopus 0/40 nucleosome Deposited 2024-06-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 20-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 3.30 Å |
| 9EAR CHD1-nucleosome complex (closed state) Deposited 2024-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Mutation：K4C C110A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K4C C110A Non-standard monomer：Yes (specific site not provided by mmCIF) | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9EGX RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27 Deposited 2024-11-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 29 PDB declaration: 32-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9EGY RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27 Deposited 2024-11-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9EGZ RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 Deposited 2024-11-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 12 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9EH0 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream Deposited 2024-11-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 9EH1 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream Deposited 2024-11-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9EH2 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream Deposited 2024-11-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9JAO The structure of SMARCAD1 bound to the hexasome in the presence of ADP-BeFx Deposited 2024-08-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric |
Chain D
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9JNP Structure of isw1-nucleosome complex in ATP state Deposited 2024-09-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 9JNT Structure of isw1-nucleosome complex in ADP* state Deposited 2024-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 9JNU Structure of isw1-nucleosome complex in ADP state Deposited 2024-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 9JNV Structure of isw1-nucleosome complex in ADP(S) state Deposited 2024-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9JNW Structure of isw1-nucleosome complex in ADP+ state Deposited 2024-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9JNX Structure of isw1-nucleosome complex in ADP*+ state Deposited 2024-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9JNZ Structure of isw1-nucleosome complex in Apo state Deposited 2024-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | CL CHLORIDE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9JO2 Structure of isw1-nucleosome complex in Apo* state Deposited 2024-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | CL CHLORIDE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9JO5 Structure of isw1-nucleosome complex in ADP-B state Deposited 2024-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9KQ2 Cryo-EM structure of RNF168'-RNF168-UbcH5c complex bound to nucleosome Deposited 2024-11-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 9LIU Structure of isw1-nucleosome double-bound complex in ATP-ATP state Deposited 2025-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 9LJ2 Structure of isw1-nucleosome double-bound complex in ADP-ADP+ state Deposited 2025-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
38–135（98 aa）
Chain E
38–135（98 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 9M76 UHRF1 bound to a mononucleosome in its pre-active state, with the RING domain bound to the SRA domain. Deposited 2025-03-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 9M77 The activated state of human UHRF1 bound to a mononucleosome, with the finger loop ordered and linker 4 disordered. Deposited 2025-03-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 9N6H 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex Deposited 2025-02-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric |
Chain A
39–136（98 aa）
Chain E
39–136（98 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.54 Å |
| 9N6I 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex Deposited 2025-02-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
37–136（100 aa）
Chain E
37–136（100 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.61 Å |
| 9Q7U Composite map for Cryo-EM structure of DNMT3A2-DNMT3B3 tetramer bound to 167H3K36me2-nucleosome Deposited 2025-08-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 9 SAO 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9UX9 local ATPase-NCP structure of the ncBAF-nucleosome complex in the ADP-BeFx-bound state Deposited 2025-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.05 Å |
| 9UXA local ARP-NCP structure of the ncBAF-nucleosome complex in the apo state Deposited 2025-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.28 Å |
| 9V2V Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with mono-nucleosome Deposited 2025-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric |
Chain Q
38–135（98 aa）
Chain U
38–135（98 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9V2W Cryo-EM structure of the histone deacetylase complex Rpd3L in complex with di-nucleosome Deposited 2025-05-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric |
Chain H
38–135（98 aa）
Chain Q
38–135（98 aa）
Chain U
38–135（98 aa）
Chain W
38–135（98 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9V33 Calypso/Asx/NCP-ub complex Deposited 2025-05-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: 15-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 5.90 Å |
| 9V9Q Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 2.80 Å |
| 9V9R Cryo-EM structure of the ncPRC1.1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.20 Å |
| 9V9S Cryo-EM structure of the ncPRC1.1 complex bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.80 Å |
| 9V9T Cryo-EM structure of the ncPRC1.6 complex bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 2.90 Å |
| 9V9U Cryo-EM structure of the ncPRC1.4 complex containing two RNF2-BMI1 bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.70 Å |
| 9V9V Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ubH2BK120ub-modified nucleosome Deposited 2025-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.80 Å |
| 9V9W Cryo-EM structure of the ncPRC1.4 complex containing two RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.00 Å |
| 9V9X Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.30 Å |
| 9V9Y Cryo-EM structure of the ncPRC1.4 complex containing one RNF2-BMI1 and one RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.20 Å |
| 9V9Z Cryo-EM structure of the ncPRC1.4 complex containing one RYBP bound to the H2AK119ub-modified nucleosome Deposited 2025-06-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.00 Å |
126 other PDB entries and 130 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | A0A310TTQ1_XENLA |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–135； UniProt 2–136 |
