Current Protein Identity：P62807
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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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 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 D
2–126（125 aa）
Chain H
2–126（125 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 |
| 5KGF Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution Deposited 2016-06-13 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric（14） Consistent with all polymers |
Chain D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；High concentration NCP-ubme/GST-53BP1 complex at 200 mM salt was diluted just prior to grid freezing.
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE；Plunged into liquid ethane-propane (FEI VITROBOT MARK III)
|
Resolution 4.54 Å |
| 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 D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 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 P
2–126（125 aa）
Chain T
2–126（125 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 |
| 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 D
1–126（126 aa）
Chain H
1–126（126 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 |
| 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 D
1–126（126 aa）
Chain H
1–126（126 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 |
| 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 D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 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 D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 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 D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 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 D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 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 D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 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 D
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 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 D
1–126（126 aa）
Chain L
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.40 Å |
| 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 D
3–126（124 aa）
Chain H
3–126（124 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 D
3–126（124 aa）
Chain H
3–126（124 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 D
3–126（124 aa）
Chain H
3–126（124 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 |
| 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 c
2–126（125 aa）
Chain g
2–126（125 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 |
| 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 D
2–126（125 aa）
Chain H
2–126（125 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 D
2–126（125 aa）
Chain H
2–126（125 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 |
| 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 D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
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 D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.44 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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.00 Å |
| 7TRF Human telomerase catalytic core RNP with H2A/H2B Deposited 2022-01-28 | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
Chain F
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 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 D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
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 D
1–126（126 aa）
Chain H
1–126（126 aa）
Chain O
1–126（126 aa）
Chain S
1–126（126 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 D
1–126（126 aa）
Chain H
1–126（126 aa）
Chain O
1–126（126 aa）
Chain S
1–126（126 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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
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 D
2–126（125 aa）
Chain H
2–126（125 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 |
| 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 D
1–126（126 aa）
Chain V
1–126（126 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 D
1–126（126 aa）
Chain h
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.90 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 P
2–126（125 aa）
Chain T
2–126（125 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 P
2–126（125 aa）
Chain T
2–126（125 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 |
| 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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 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 Ba
1–126（126 aa）
Chain Bb
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20 mM HEPES pH 7.5, 50 mM NaCl and 1 mM DTT
cryo-EM vitrification conditions
Cryogen ETHANE；blot force = 0 N
blot time = 8 s
|
Resolution 3.40 Å |
| 8OO7 CryoEM Structure INO80core Hexasome complex composite model state1 Deposited 2023-04-04 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: 18-meric（18） Consistent with all polymers |
Chain P
2–126（125 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 P
2–126（125 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 P
2–126（125 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 P
2–126（125 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 |
| 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 D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8；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 D
1–126（126 aa）
Chain H
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8；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 |
| 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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；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 |
| 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 D
1–124（124 aa）
Chain H
1–124（124 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 D
1–124（124 aa）
Chain H
1–124（124 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 D
1–124（124 aa）
Chain H
1–124（124 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 D
1–124（124 aa）
Chain H
1–124（124 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 |
| 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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；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 |
| 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 B
1–126（126 aa）
Chain F
1–126（126 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 B
1–126（126 aa）
Chain F
1–126（126 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 B
1–126（126 aa）
Chain F
1–126（126 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 |
| 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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.1；25mM HEPES (pH-7.1), 50mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 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 H
2–126（125 aa）
Chain M
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 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 D
2–126（125 aa）
Chain H
2–126（125 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 |
| 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 f
1–126（126 aa）
Chain j
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 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 D
1–126（126 aa）
Chain J
1–126（126 aa）
Chain f
1–126（126 aa）
Chain j
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 15.50 Å |
| 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 D
1–126（126 aa）
Chain H
1–126（126 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 D
1–126（126 aa）
Chain H
1–126（126 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 D
1–126（126 aa）
Chain H
1–126（126 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 D
1–126（126 aa）
Chain H
1–126（126 aa）
Chain P
1–126（126 aa）
Chain R
1–126（126 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 D
1–126（126 aa）
Chain H
1–126（126 aa）
Chain N
1–126（126 aa）
Chain P
1–126（126 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 D
1–126（126 aa）
Chain H
1–126（126 aa）
Chain N
1–126（126 aa）
Chain P
1–126（126 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY | mmCIF provides none of the parsed conditions | Resolution 3.40 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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
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 D
2–126（125 aa）
Chain H
2–126（125 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.74 Å |