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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P0C0S8 New Search
50PDB entries
53Biological assembly
100chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
10YE DNA Ligase IIIa bound to nucleosome containing a nick at SHL0 Deposited 2026-02-12 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric（12） Consistent with all polymers
Chain C 12–119（108 aa）
Chain G 12–119（108 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
10YG DNA Ligase IIIa bound to a nucleosome containing a nick at SHL-4 (composite) Deposited 2026-02-12 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric（12） Consistent with all polymers
Chain C 12–119（108 aa）
Chain G 12–119（108 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution not provided
4QYL Crystal Structure of the human BRPF1 bromodomain in complex with a histone H2AK5ac peptide Deposited 2014-07-24 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain E 2–13（12 aa） Fragment：histone H2AK5ac peptide (UNP residues 2-13)
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M NH4SO4, 0.1 M MES monohydrate, pH 6.5, 30% w/v polyethylene glycol monomethyl ether (PEG) 5000, 1% propylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.253
4QYL Crystal Structure of the human BRPF1 bromodomain in complex with a histone H2AK5ac peptide Deposited 2014-07-24 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain F 2–13（12 aa） Fragment：histone H2AK5ac peptide (UNP residues 2-13)
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M NH4SO4, 0.1 M MES monohydrate, pH 6.5, 30% w/v polyethylene glycol monomethyl ether (PEG) 5000, 1% propylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.253
4QYL Crystal Structure of the human BRPF1 bromodomain in complex with a histone H2AK5ac peptide Deposited 2014-07-24 Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain G 2–13（12 aa） Fragment：histone H2AK5ac peptide (UNP residues 2-13)
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M NH4SO4, 0.1 M MES monohydrate, pH 6.5, 30% w/v polyethylene glycol monomethyl ether (PEG) 5000, 1% propylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.253
4QYL Crystal Structure of the human BRPF1 bromodomain in complex with a histone H2AK5ac peptide Deposited 2014-07-24 Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain H 2–13（12 aa） Fragment：histone H2AK5ac peptide (UNP residues 2-13)
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M NH4SO4, 0.1 M MES monohydrate, pH 6.5, 30% w/v polyethylene glycol monomethyl ether (PEG) 5000, 1% propylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.253
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 C 1–130（130 aa）
Chain G 1–130（130 aa）
Mutation：K13R, T16S, K36R Mutation：K13R, T16S, K36R 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
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 C 1–130（130 aa）
Chain G 1–130（130 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 C 1–130（130 aa）
Chain G 1–130（130 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
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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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
7E8D NSD2 E1099K mutant bound to nucleosome Deposited 2021-03-01 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 3 SFG SINEFUNGIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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
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 C 2–130（129 aa）
Chain G 2–130（129 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
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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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
8GUI Bre1-nucleosome complex (Model I) Deposited 2022-09-12 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
8GUJ Bre1-nucleosome complex (Model II) Deposited 2022-09-12 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8GUK Human nucleosome core particle (free form) Deposited 2022-09-12 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.51 Å
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 Aa 1–130（130 aa）
Chain Ab 1–130（130 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
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 C 2–130（129 aa）
Chain G 2–130（129 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
8VOB H3K36me3-modified nucleosome bound to PRC2_AJ1-450 Deposited 2024-01-14 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain K 13–120（108 aa）
Chain R 13–120（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8VWS Nucleosome containing 8oxoG at SHL-6 Deposited 2024-02-02 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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
9BE5 Cryo-EM structure of Human Nucleosome collected by EPU on Glacios at 3.3 Angstrom resolution Deposited 2024-04-14 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain C 17–119（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9BE6 Cryo-EM structure of Human Nucleosome collected by Leginon on Krios at 3.0 Angstrom resolution Deposited 2024-04-14 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain C 17–119（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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
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 C 2–130（129 aa）
Chain G 2–130（129 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
9SI3 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome Deposited 2025-08-28 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
9SI9 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class0) Deposited 2025-08-28 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
9SJ5 Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Class1) Deposited 2025-08-29 Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
9SLJ Chromosomal Passenger Complex in complex with H3T3ph Nucleosome (Double Occupancy) Deposited 2025-09-04 Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: 16-meric（16） Consistent with all polymers
Chain C 2–130（129 aa）
Chain G 2–130（129 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
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 C 2–130（129 aa）
Chain G 2–130（129 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 C 2–130（129 aa）
Chain G 2–130（129 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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.