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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：P84040 New Search
19PDB entries
21Biological assembly
39chain/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
2NQB Drosophila Nucleosome Structure Deposited 2006-10-30 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain B 1–102（102 aa）
Chain F 1–102（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；Constituents of the crystallization buffer: Potassium Chloride, Manganese Chloride, and Potassium Cacodylate., pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.30 Å R-free 0.254
2PYO Drosophila nucleosome core Deposited 2007-05-16 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded MN MANGANESE (II) ION × 14 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；Crystallization was carried out by equilibrating a droplet containing 3 mg/ml nucleosome core particle, 80-85 mM MnCl2, 50-80 mM KCl and 20 mM potassium cacodylate (pH 6.0) against a reservoir solution containing of 40-42.5 mM MnCl2, 25-40 mM KCl and 20 mM potassium cacodylate (pH 6.0). , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.43 Å R-free 0.262
2XYI Crystal Structure of Nurf55 in complex with a H4 peptide Deposited 2010-11-17 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 27–46（20 aa） Fragment：RESIDUES 27-46
Not recorded PG4 TETRAETHYLENE GLYCOL × 3 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；35%(V/V) PEG 400, 100MM MES PH 6
Resolution 1.75 Å R-free 0.195
3C9C Structural Basis of Histone H4 Recognition by p55 Deposited 2008-02-15 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 16–42（27 aa） Fragment：UNP residues 16-42
Not recorded CD CADMIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.242
4QLC Crystal structure of chromatosome at 3.5 angstrom resolution Deposited 2014-06-11 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded CIT CITRIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.75；291 K；0.1 mM Citric acid, 0.1mM potassium chloride, and 10% MPD, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.50 Å R-free 0.243
4UUZ MCM2-histone complex Deposited 2014-08-01 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain B 1–103（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M HEPES PH7, 21% PEG3000
Resolution 2.90 Å R-free 0.230
4X23 CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE Deposited 2014-11-25 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain B 25–103（79 aa） Fragment：UNP RESIDUES 25-103
Chain F 25–103（79 aa） Fragment：UNP RESIDUES 25-103
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；10% MPD, 40MM SODIUM CACODYLATE, 24MM SPERMINE TETRA-HCL, 80MM SODIUM CHLORIDE, 20MM MAGNESIUM CHLORIDE; RESERVIOR 35% MPD. PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K
Resolution 3.50 Å R-free 0.286
4X23 CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE Deposited 2014-11-25 Assembly 2 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain L 25–103（79 aa） Fragment：UNP RESIDUES 25-103
Chain P 25–103（79 aa） Fragment：UNP RESIDUES 25-103
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；10% MPD, 40MM SODIUM CACODYLATE, 24MM SPERMINE TETRA-HCL, 80MM SODIUM CHLORIDE, 20MM MAGNESIUM CHLORIDE; RESERVIOR 35% MPD. PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K
Resolution 3.50 Å R-free 0.286
5WCU Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5 Deposited 2017-07-02 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain B 22–103（82 aa） Fragment：UNP residues 22-103
Chain F 22–103（82 aa） Fragment：UNP residues 22-103
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；291 K；0.1 M NH4NO3, 10% MPD (v/v)
Resolution 5.53 Å R-free 0.238
5WCU Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5 Deposited 2017-07-02 Assembly 2 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers
Chain L 22–103（82 aa） Fragment：UNP residues 22-103
Chain P 22–103（82 aa） Fragment：UNP residues 22-103
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；291 K；0.1 M NH4NO3, 10% MPD (v/v)
Resolution 5.53 Å R-free 0.238
6DZT Cryo-EM structure of nucleosome in complex with a single chain antibody fragment Deposited 2018-07-05 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å
7XYF Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome Deposited 2022-06-01 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers
Chain B 18–103（86 aa）
Chain F 18–103（86 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XYG Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome Deposited 2022-06-01 Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers
Chain B 1–103（103 aa）
Chain F 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8UX1 Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle Deposited 2023-11-08 Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers
Chain B 2–103（102 aa）
Chain F 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9MU4 Structure of a native Drosophila melanogaster octameric nucleosome Deposited 2025-01-13 Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers
Chain b 22–103（82 aa）
Chain f 22–103（82 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.29 Å
9MU5 Structure of a native Drosophila melanogaster hexameric nucleosome Deposited 2025-01-13 Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric（8） Consistent with all polymers
Chain b 24–103（80 aa）
Chain f 24–103（80 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
9MU9 Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Deposited 2025-01-13 Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric（21） Consistent with all polymers
Chain b 24–103（80 aa）
Chain f 24–103（80 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.80 Å
9ZQ9 Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 1 Deposited 2025-12-18 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric（14） Consistent with all polymers
Chain G 2–103（102 aa）
Chain H 2–103（102 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9ZQA Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 2 Deposited 2025-12-18 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric（14） Consistent with all polymers
Chain G 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.28 Å
9ZQB Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1 Deposited 2025-12-18 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric（14） Consistent with all polymers
Chain G 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.10 Å
9ZQC Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2 Deposited 2025-12-18 Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric（14） Consistent with all polymers
Chain G 1–103（103 aa）
Chain H 1–103（103 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.37 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.