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9zqc

Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2

Method: ELECTRON MICROSCOPY Dmax: 131.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone H2A

Drosophila melanogaster

UniProt P84051

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 × 11 DNA 3 PDB declaration: 14-meric（14） Consistent with all polymer counts Chain A； UniProt 1–124 Chain B； UniProt 1–124 Not recorded Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） mAb PL2-6 antibody × 2 DNA (60-MER) × 1 DNA (128-MER) × 1 DNA (197-MER) × 1 Poly [ADP-ribose] polymerase 2 × 1 （Q9UGN5） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.37 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 9ZQC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2NQB Drosophila Nucleosome Structure Deposited 2006-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–123（123 aa）
Chain G 1–123（123 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 Different construct 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 C 2–121（120 aa）
Chain G 2–121（120 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
4QLC Crystal structure of chromatosome at 3.5 angstrom resolution Deposited 2014-06-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 2–124（123 aa）
Chain G 2–124（123 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
4X23 CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE Deposited 2014-11-25 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 16–117（102 aa） Fragment：UNP RESIDUES 16-117
Chain G 16–117（102 aa） Fragment：UNP RESIDUES 16-117
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 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain M 16–117（102 aa） Fragment：UNP RESIDUES 16-117
Chain Q 16–117（102 aa） Fragment：UNP RESIDUES 16-117
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 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 15–118（104 aa） Fragment：UNP residues 15-118
Chain G 15–118（104 aa） Fragment：UNP residues 15-118
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 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain M 15–118（104 aa） Fragment：UNP residues 15-118
Chain Q 15–118（104 aa） Fragment：UNP residues 15-118
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 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–124（124 aa）
Chain G 1–124（124 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
6PWE Cryo-EM structure of nucleosome core particle Deposited 2019-07-22 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–124（124 aa）
Chain G 1–124（124 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
6PWF Cryo-EM structure of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome Deposited 2019-07-22 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain C 1–124（124 aa）
Chain G 1–124（124 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7PJ1 Solution structure of isolated Drosophila histone H2A-H2B heterodimer Deposited 2021-08-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–124（123 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 300；Pressure 1
NMR sample composition 0.5 mM histone H2A, 0.5 mM [U-15N; U-2H] histone H2B, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7XYF Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome Deposited 2022-06-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 14–119（106 aa）
Chain G 14–119（106 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 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain C 2–124（123 aa）
Chain G 2–124（123 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
8PP6 human RYBP-PRC1 bound to H2AK118ub1 nucleosome Deposited 2023-07-06 Different construct 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 C 2–124（123 aa）
Chain G 2–124（123 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
8PP7 human RYBP-PRC1 bound to mononucleosome Deposited 2023-07-06 Different construct 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 C 2–124（123 aa）
Chain G 2–124（123 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
8UX1 Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle Deposited 2023-11-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain C 1–124（124 aa）
Chain G 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 2.50 Å
9MU4 Structure of a native Drosophila melanogaster octameric nucleosome Deposited 2025-01-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain c 14–119（106 aa）
Chain g 14–119（106 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 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain g 14–118（105 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 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain c 14–119（106 aa）
Chain g 14–119（106 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 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain A 1–124（124 aa）
Chain B 1–124（124 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 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain A 1–124（124 aa）
Chain B 1–124（124 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 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain A 1–124（124 aa）
Chain B 1–124（124 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

20 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H2A_DROME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–124； UniProt 1–124 Author chain B； PDBConstruct 1–124； UniProt 1–124

Histone H2B

Drosophila melanogaster

UniProt P02283

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 × 11 DNA 3 PDB declaration: 14-meric（14） Consistent with all polymer counts Chain C； UniProt 1–123 Chain D； UniProt 1–123 Not recorded Histone H2A × 2 （P84051） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） mAb PL2-6 antibody × 2 DNA (60-MER) × 1 DNA (128-MER) × 1 DNA (197-MER) × 1 Poly [ADP-ribose] polymerase 2 × 1 （Q9UGN5） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.37 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 9ZQC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2NQB Drosophila Nucleosome Structure Deposited 2006-10-30 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–123（123 aa）
Chain H 1–123（123 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 Different construct 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 D 2–123（122 aa）
Chain H 2–123（122 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
4QLC Crystal structure of chromatosome at 3.5 angstrom resolution Deposited 2014-06-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 2–123（122 aa）
Chain H 2–123（122 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
4X23 CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE Deposited 2014-11-25 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 33–122（90 aa） Fragment：UNP RESIDUES 33-122
Chain H 33–122（90 aa） Fragment：UNP RESIDUES 33-122
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 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain N 33–122（90 aa） Fragment：UNP RESIDUES 33-122
Chain R 33–122（90 aa） Fragment：UNP RESIDUES 33-122
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
5CVE Crystal Structure of human NRMT1 in complex with dimethylated fly H2B peptide and SAH Deposited 2015-07-26 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 × 2 PDB declaration: dimeric
Chain D 2–10（9 aa） Fragment：UNP residues 2-10
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.7；291 K；0.2 M (NH4)Ac, 0.1 M Sodium citrate tribasic dihydrate, 24%(w/v) PEG 4000
Resolution 1.50 Å R-free 0.179
5CVE Crystal Structure of human NRMT1 in complex with dimethylated fly H2B peptide and SAH Deposited 2015-07-26 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 × 2 PDB declaration: dimeric
Chain E 2–10（9 aa） Fragment：UNP residues 2-10
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.7；291 K；0.2 M (NH4)Ac, 0.1 M Sodium citrate tribasic dihydrate, 24%(w/v) PEG 4000
Resolution 1.50 Å R-free 0.179
5WCU Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5 Deposited 2017-07-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 29–122（94 aa） Fragment：UNP residues 29-122
Chain H 29–122（94 aa） Fragment：UNP residues 29-122
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 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain N 29–122（94 aa） Fragment：UNP residues 29-122
Chain R 29–122（94 aa） Fragment：UNP residues 29-122
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 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 2–123（122 aa）
Chain H 2–123（122 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
6PWE Cryo-EM structure of nucleosome core particle Deposited 2019-07-22 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain D 1–123（123 aa）
Chain H 1–123（123 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
6PWF Cryo-EM structure of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome Deposited 2019-07-22 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain D 1–123（123 aa）
Chain H 1–123（123 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7PJ1 Solution structure of isolated Drosophila histone H2A-H2B heterodimer Deposited 2021-08-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–123（122 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 300；Pressure 1
NMR sample composition 0.5 mM histone H2A, 0.5 mM [U-15N; U-2H] histone H2B, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7XYF Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome Deposited 2022-06-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 29–123（95 aa）
Chain H 29–123（95 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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain D 1–123（123 aa）
Chain H 1–123（123 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
8PP6 human RYBP-PRC1 bound to H2AK118ub1 nucleosome Deposited 2023-07-06 Different construct 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 D 2–123（122 aa）
Chain H 2–123（122 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
8PP7 human RYBP-PRC1 bound to mononucleosome Deposited 2023-07-06 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 D 1–123（123 aa）
Chain H 1–123（123 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
8UX1 Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle Deposited 2023-11-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain D 1–123（123 aa）
Chain H 1–123（123 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 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain d 27–123（97 aa）
Chain h 27–123（97 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 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain h 27–123（97 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 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain d 27–123（97 aa）
Chain h 27–123（97 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 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain C 2–123（122 aa）
Chain D 2–123（122 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 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain C 1–123（123 aa）
Chain D 1–123（123 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 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain C 1–123（123 aa）
Chain D 1–123（123 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

21 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H2B_DROME
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 2–125； UniProt 1–123 Author chain D； PDBConstruct 2–125； UniProt 1–123

Histone H3

Drosophila melanogaster

UniProt P02299

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 × 11 DNA 3 PDB declaration: 14-meric（14） Consistent with all polymer counts Chain E； UniProt 1–136 Chain F； UniProt 1–136 Mutation：C111S Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H4 × 2 （P84040） mAb PL2-6 antibody × 2 DNA (60-MER) × 1 DNA (128-MER) × 1 DNA (197-MER) × 1 Poly [ADP-ribose] polymerase 2 × 1 （Q9UGN5） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.37 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 9ZQC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1KNA Chromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9. Deposited 2001-12-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 1–16（16 aa） Fragment：Residues 1-16
Mutation：P16Y Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；283 K；Ammonium Sulfate, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 283.0K
Resolution 2.10 Å R-free 0.259
1KNE Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9 Deposited 2001-12-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 1–16（16 aa） Fragment：Residues 1-16
Mutation：P16Y Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；283 K；Ammonium Sulfate, MES, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Resolution 2.40 Å R-free 0.267
2NQB Drosophila Nucleosome Structure Deposited 2006-10-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–135（135 aa）
Chain E 1–135（135 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 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 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
2YBA Crystal structure of Nurf55 in complex with histone H3 Deposited 2011-03-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–20（19 aa） Fragment：N-TERMINAL TAIL, RESIDUES 2-19
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 100 MM SODIUM CITRATE, PH 5.4; 200 MM AMMONIUM ACETATE; 23% PEG 3350.
Resolution 2.55 Å R-free 0.222
2YBA Crystal structure of Nurf55 in complex with histone H3 Deposited 2011-03-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–20（19 aa） Fragment：N-TERMINAL TAIL, RESIDUES 2-19
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 100 MM SODIUM CITRATE, PH 5.4; 200 MM AMMONIUM ACETATE; 23% PEG 3350.
Resolution 2.55 Å R-free 0.222
4QLC Crystal structure of chromatosome at 3.5 angstrom resolution Deposited 2014-06-11 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 × 9 PDB declaration: undecameric
Chain A 2–136（135 aa）
Chain E 2–136（135 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
4U68 Crystal structure of Rhino chromodomain in complex with H3K9me3 Deposited 2014-07-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 5–15（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；290 K；30 %(v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, 25 % (w/v) PEG 1500
Resolution 1.80 Å R-free 0.206
4U68 Crystal structure of Rhino chromodomain in complex with H3K9me3 Deposited 2014-07-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 5–15（11 aa）
Chain F 5–15（11 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 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；290 K；30 %(v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, 25 % (w/v) PEG 1500
Resolution 1.80 Å R-free 0.206
4UUZ MCM2-histone complex Deposited 2014-08-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–136（136 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 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 41–133（93 aa） Fragment：UNP RESIDUES 41-133
Chain E 41–133（93 aa） Fragment：UNP RESIDUES 41-133
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 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 41–133（93 aa） Fragment：UNP RESIDUES 41-133
Chain O 41–133（93 aa） Fragment：UNP RESIDUES 41-133
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 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 39–136（98 aa） Fragment：UNP residues 39-136
Chain E 39–136（98 aa） Fragment：UNP residues 39-136
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 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 39–136（98 aa） Fragment：UNP residues 39-136
Chain O 39–136（98 aa） Fragment：UNP residues 39-136
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 Different mutation/modification Different oligomeric state 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
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å
6PWE Cryo-EM structure of nucleosome core particle Deposited 2019-07-22 Different mutation/modification Different oligomeric state 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 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
6PWF Cryo-EM structure of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome Deposited 2019-07-22 Different mutation/modification Different oligomeric state 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 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7VRF Crystal structure of Oxpecker chromodomain in complex with H3K9me3 Deposited 2021-10-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 5–15（11 aa）
Chain D 5–15（11 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 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；0.2M ammonium citrate, 20% (w/v) PEG 3350
Resolution 1.70 Å R-free 0.238
7XYF Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome Deposited 2022-06-01 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
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
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 Different construct Different mutation/modification Different oligomeric state 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 No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9B1E Cryo-EM structure of native SWR1 bound to nucleosome (composite structure) Deposited 2024-03-13 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 U 1–136（136 aa）
Chain W 1–136（136 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；80 nM SWR1, 160 nM nucleosomes, 1 mM ADP, 10 mM NaF, 8 mM BeCl2, 0.05% glutaraldehyde, 20 mM HEPES-KOH pH 7.6, 1.5 mM MgCl2, 0.25 mM TCEP, 0.01% IGEPAL CA-630, 1% glycerol
cryo-EM vitrification conditions Cryogen ETHANE；3 second blot time and blot force of 10.
Resolution 4.40 Å
9MU4 Structure of a native Drosophila melanogaster octameric nucleosome Deposited 2025-01-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
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；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 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
Chain a 45–136（92 aa）
Chain e 45–136（92 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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain a 37–136（100 aa）
Chain e 37–136（100 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 Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain E 1–136（136 aa）
Chain F 1–136（136 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 Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain E 1–136（136 aa）
Chain F 1–136（136 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 Different mutation/modification Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain E 1–136（136 aa）
Chain F 1–136（136 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

23 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H3_DROME
Isoform —
PDB entities 3
Chains and sequence ranges Author chain E； PDBConstruct 1–136； UniProt 1–136 Author chain F； PDBConstruct 1–136； UniProt 1–136

Histone H4

Drosophila melanogaster

UniProt P84040

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 × 11 DNA 3 PDB declaration: 14-meric（14） Consistent with all polymer counts Chain G； UniProt 1–103 Chain H； UniProt 1–103 Not recorded Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） mAb PL2-6 antibody × 2 DNA (60-MER) × 1 DNA (128-MER) × 1 DNA (197-MER) × 1 Poly [ADP-ribose] polymerase 2 × 1 （Q9UGN5） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.37 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 9ZQC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2NQB Drosophila Nucleosome Structure Deposited 2006-10-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
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 Different construct 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 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 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 × 2 PDB declaration: dimeric
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 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 × 2 PDB declaration: dimeric
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 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
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 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
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 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
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 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
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 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
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 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
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 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
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 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
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 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric
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 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
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 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
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 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric
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 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
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 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
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 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
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 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
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

18 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H4_DROME
Isoform —
PDB entities 4
Chains and sequence ranges Author chain G； PDBConstruct 1–104； UniProt 1–103 Author chain H； PDBConstruct 1–104； UniProt 1–103

Poly [ADP-ribose] polymerase 2

Homo sapiens

UniProt Q9UGN5

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 × 11 DNA 3 PDB declaration: 14-meric（14） Consistent with all polymer counts Chain P； UniProt 90–583 Not recorded Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） mAb PL2-6 antibody × 2 DNA (60-MER) × 1 DNA (128-MER) × 1 DNA (197-MER) × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.37 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 9ZQC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3KCZ Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor 3-aminobenzamide Deposited 2009-10-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 235–579（345 aa） Fragment：Catalytic domain
Not recorded 3AB 3-aminobenzamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；22% PEG 3350, 0.1M Tris-HCl, 0.01M 3-aminobenzamide, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.00 Å R-free 0.237
3KCZ Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor 3-aminobenzamide Deposited 2009-10-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 235–579（345 aa） Fragment：Catalytic domain
Not recorded 3AB 3-aminobenzamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；22% PEG 3350, 0.1M Tris-HCl, 0.01M 3-aminobenzamide, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.00 Å R-free 0.237
3KJD Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor ABT-888 Deposited 2009-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 235–579（345 aa） Fragment：catalytic domain
Not recorded 78P (2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 3350, 0.1M Tris, 0.25M NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.95 Å R-free 0.232
3KJD Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor ABT-888 Deposited 2009-11-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 235–579（345 aa） Fragment：catalytic domain
Not recorded 78P (2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG 3350, 0.1M Tris, 0.25M NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.95 Å R-free 0.232
4PJV Structure of PARP2 catalytic domain bound to inhibitor BMN 673 Deposited 2014-05-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 235–579（345 aa） Fragment：PARP2 HELICAL AND CATALYTIC DOMAINS (UNP residues 235-579)
Not recorded 2YQ (8S,9R)-5-fluoro-8-(4-fluorophenyl)-9-(1-methyl-1H-1,2,4-triazol-5-yl)-2,7,8,9-tetrahydro-3H-pyrido[4,3,2-de]phthalazin-3-one × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；(W/V) POLYETHYLENE GLYCOL 3350, 333 mM SODIUM CHLORIDE.
Resolution 2.50 Å R-free 0.287
4PJV Structure of PARP2 catalytic domain bound to inhibitor BMN 673 Deposited 2014-05-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 235–579（345 aa） Fragment：PARP2 HELICAL AND CATALYTIC DOMAINS (UNP residues 235-579)
Not recorded 2YQ (8S,9R)-5-fluoro-8-(4-fluorophenyl)-9-(1-methyl-1H-1,2,4-triazol-5-yl)-2,7,8,9-tetrahydro-3H-pyrido[4,3,2-de]phthalazin-3-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；(W/V) POLYETHYLENE GLYCOL 3350, 333 mM SODIUM CHLORIDE.
Resolution 2.50 Å R-free 0.287
4TVJ HUMAN ARTD2 (PARP2) - CATALYTIC DOMAIN IN COMPLEX WITH OLAPARIB Deposited 2014-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain A 235–579（345 aa）
Not recorded 09L 4-(3-{[4-(cyclopropylcarbonyl)piperazin-1-yl]carbonyl}-4-fluorobenzyl)phthalazin-1(2H)-one × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG3350, 0.1M Tris
Resolution 2.10 Å R-free 0.231
4TVJ HUMAN ARTD2 (PARP2) - CATALYTIC DOMAIN IN COMPLEX WITH OLAPARIB Deposited 2014-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric
Chain B 235–579（345 aa）
Not recorded 09L 4-(3-{[4-(cyclopropylcarbonyl)piperazin-1-yl]carbonyl}-4-fluorobenzyl)phthalazin-1(2H)-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；25% PEG3350, 0.1M Tris
Resolution 2.10 Å R-free 0.231
4ZZX Structure of PARP2 catalytic domain bound to an isoindolinone inhibitor Deposited 2015-04-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 223–583（361 aa） Fragment：CATALYTIC DOMAIN, UNP RESIDUES 223-583
Not recorded FSU 2-(3-methoxypropyl)-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；25% PEG4000, 0.2M MAGNESIUM CHLORIDE, 0.1 M TRIS PH 8.5, 277K
Resolution 1.65 Å R-free 0.244
4ZZX Structure of PARP2 catalytic domain bound to an isoindolinone inhibitor Deposited 2015-04-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 223–583（361 aa） Fragment：CATALYTIC DOMAIN, UNP RESIDUES 223-583
Not recorded FSU 2-(3-methoxypropyl)-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；25% PEG4000, 0.2M MAGNESIUM CHLORIDE, 0.1 M TRIS PH 8.5, 277K
Resolution 1.65 Å R-free 0.244
4ZZY Structure of human PARP2 catalytic domain bound to an isoindolinone inhibitor Deposited 2015-04-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 223–583（361 aa） Fragment：CATALYTIC DOMAIN, UNP RESIDUES 223-583
Not recorded D7N 2-[1-(4,4-Difluorocyclohexyl)-piperidin-4-yl]-6-fluoro-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 25% PEG4000, 0.2M MAGNESIUM CLORIDE, 0.1 M TRIS PH 8.5
Resolution 2.20 Å R-free 0.280
5D5K Crystal Structure NLS from human PARP-2 complexed with Importin alpha delta IBB Deposited 2015-08-10 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–78（78 aa） Fragment：unp residues 1-78
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；0.6-0.7M sodium citrate, 0.1M sodium citrate buffer pH 5.6, and 7-10mM DTT
Resolution 1.90 Å R-free 0.171
5DSY Crystal structure of constitutively active PARP-2 Deposited 2015-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 348–583（236 aa） Fragment：unp residues 348-583
Not recorded UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；2.55-2.65 M NaCl and 0.1 M Tris
Resolution 2.70 Å R-free 0.248
5DSY Crystal structure of constitutively active PARP-2 Deposited 2015-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 348–583（236 aa） Fragment：unp residues 348-583
Not recorded UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；2.55-2.65 M NaCl and 0.1 M Tris
Resolution 2.70 Å R-free 0.248
5DSY Crystal structure of constitutively active PARP-2 Deposited 2015-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 348–583（236 aa） Fragment：unp residues 348-583
Not recorded UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；2.55-2.65 M NaCl and 0.1 M Tris
Resolution 2.70 Å R-free 0.248
5DSY Crystal structure of constitutively active PARP-2 Deposited 2015-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 348–583（236 aa） Fragment：unp residues 348-583
Not recorded UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；2.55-2.65 M NaCl and 0.1 M Tris
Resolution 2.70 Å R-free 0.248
6F1K Structure of ARTD2/PARP2 WGR domain bound to double strand DNA without 5'phosphate Deposited 2017-11-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 90–218（129 aa）
Not recorded GOL GLYCEROL × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；277 K；PEG MME 5000 0.1 M Na-acetate ethylene glyco
Resolution 2.20 Å R-free 0.250
6F5B Structure of ARTD2/PARP2 WGR domain bound to double stranded DNA with 5'phosphate Deposited 2017-12-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 90–218（129 aa）
Chain B 90–218（129 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；277 K；12 % v/v Polypropylene glycol 400 0.1 M Na-acetate 3 % 2 propanol
Resolution 2.80 Å R-free 0.274
6F5F Structure of ARTD2/PARP2 WGR domain bound to double strand DNA with 5 nucleotide overhang and 5'phosphate Deposited 2017-12-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 90–218（129 aa）
Chain C 90–218（129 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Na-formate 20 % PEG 3350 20 % glycerol
Resolution 2.98 Å R-free 0.275
6F5F Structure of ARTD2/PARP2 WGR domain bound to double strand DNA with 5 nucleotide overhang and 5'phosphate Deposited 2017-12-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain B 90–218（129 aa）
Chain D 90–218（129 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Na-formate 20 % PEG 3350 20 % glycerol
Resolution 2.98 Å R-free 0.275
6TX3 HPF1 bound to catalytic fragment of PARP2 Deposited 2020-01-13 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 × 2 PDB declaration: dimeric
Chain B 230–253（24 aa）
Chain B 348–583（236 aa）
Not recorded UHB 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES pH 6, 25% v/v pentaerythritol propoxylate (5/4 PO/OH)
Resolution 2.96 Å R-free 0.260
6USJ Structure of two nucleosomes bridged by human PARP2 Deposited 2019-10-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain U 1–570（570 aa）
Chain V 1–570（570 aa）
Mutation：Q112R, F113D Mutation：Q112R, F113D No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Buffer was pH-adjusted and filtered through a 0.22 um filter.
cryo-EM vitrification conditions Cryogen ETHANE；Blot time 2s, blot force 0
Resolution 10.50 Å
6X0L Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain P 1–570（570 aa）
Chain R 1–570（570 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6X0M Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain P 1–570（570 aa）
Chain p 1–570（570 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
6X0N Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin Deposited 2020-05-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 23-meric
Chain P 1–570（570 aa）
Chain R 1–570（570 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 10.00 Å
7AEO Human ARTD2 in complex with DNA oligonucleotides Deposited 2020-09-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 90–583（494 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Sample was crystallized in 0.1 M MES pH 6.5 and 1 M ammonium sulfate. Cryo solution was a mixture of 10% (v/v) glycerol, 10% (v/v) diethylene glycol, and 10% (v/v) 2-propanol with the crystallization conditions
Resolution 2.80 Å R-free 0.271
7R59 PARP2 catalytic domain in complex with OUL245 Deposited 2022-02-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 235–583（349 aa）
Not recorded GOL GLYCEROL × 1 I5F [1,2,4]triazolo[3,4-b][1,3]benzothiazol-6-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100 mM Tris pH 9.5 and 20% PEG 3350
Resolution 2.00 Å R-free 0.238
8HE8 Human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor Deposited 2022-11-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 231–581（351 aa）
Not recorded GOL GLYCEROL × 1 1WI 1-[[4-fluoranyl-3-(3-oxidanylidene-4-pentan-3-yl-piperazin-1-yl)carbonyl-phenyl]methyl]quinazoline-2,4-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.3-8.5
Resolution 3.05 Å R-free 0.256
8HE8 Human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor Deposited 2022-11-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 231–581（351 aa）
Not recorded GOL GLYCEROL × 1 1WI 1-[[4-fluoranyl-3-(3-oxidanylidene-4-pentan-3-yl-piperazin-1-yl)carbonyl-phenyl]methyl]quinazoline-2,4-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.3-8.5
Resolution 3.05 Å R-free 0.256
8HE8 Human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor Deposited 2022-11-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 231–581（351 aa）
Not recorded 1WI 1-[[4-fluoranyl-3-(3-oxidanylidene-4-pentan-3-yl-piperazin-1-yl)carbonyl-phenyl]methyl]quinazoline-2,4-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.3-8.5
Resolution 3.05 Å R-free 0.256
8HKN Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to approved drug Fluzoparib Deposited 2022-11-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 1 25I Fluzoparib × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.50 Å R-free 0.261
8HKN Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to approved drug Fluzoparib Deposited 2022-11-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 1 25I Fluzoparib × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.50 Å R-free 0.261
8HKO Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Rucaparib Deposited 2022-11-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 5 RPB Rucaparib × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.10 Å R-free 0.211
8HKO Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Rucaparib Deposited 2022-11-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 1 RPB Rucaparib × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.10 Å R-free 0.211
8HKS Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Pamiparib(BGB-290) Deposited 2022-11-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 2 DS9 (2R)-14-fluoro-2-methyl-6,9,10,19-tetrazapentacyclo[14.2.1.02,6.08,18.012,17]nonadeca-1(18),8,12(17),13,15-pentaen-11-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.80 Å R-free 0.238
8HKS Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Pamiparib(BGB-290) Deposited 2022-11-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 5 DS9 (2R)-14-fluoro-2-methyl-6,9,10,19-tetrazapentacyclo[14.2.1.02,6.08,18.012,17]nonadeca-1(18),8,12(17),13,15-pentaen-11-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.80 Å R-free 0.238
8HKS Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Pamiparib(BGB-290) Deposited 2022-11-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 2 DS9 (2R)-14-fluoro-2-methyl-6,9,10,19-tetrazapentacyclo[14.2.1.02,6.08,18.012,17]nonadeca-1(18),8,12(17),13,15-pentaen-11-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.80 Å R-free 0.238
8HKS Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Pamiparib(BGB-290) Deposited 2022-11-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 3 DS9 (2R)-14-fluoro-2-methyl-6,9,10,19-tetrazapentacyclo[14.2.1.02,6.08,18.012,17]nonadeca-1(18),8,12(17),13,15-pentaen-11-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.80 Å R-free 0.238
8HLJ Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Olaparib (AZD2281) Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L 09L 4-(3-{[4-(cyclopropylcarbonyl)piperazin-1-yl]carbonyl}-4-fluorobenzyl)phthalazin-1(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296.5 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.24 Å R-free 0.247
8HLJ Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Olaparib (AZD2281) Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L 09L 4-(3-{[4-(cyclopropylcarbonyl)piperazin-1-yl]carbonyl}-4-fluorobenzyl)phthalazin-1(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296.5 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.24 Å R-free 0.247
8HLQ Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Niraparib (MK-4827) Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 1 3JD 2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.70 Å R-free 0.282
8HLQ Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Niraparib (MK-4827) Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 2 3JD 2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.70 Å R-free 0.282
8JNY Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a pyrazolopyrimidine carboxamide inhibitor Deposited 2023-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L ERV 6-methylpyrazolo[1,5-a]pyrimidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 3.20 Å R-free 0.268
8JNY Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a pyrazolopyrimidine carboxamide inhibitor Deposited 2023-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L ERV 6-methylpyrazolo[1,5-a]pyrimidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 3.20 Å R-free 0.268
9IM8 Mutated ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a pyrimidine 2,4-diketone derivative inhibitor Deposited 2024-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L GOL GLYCEROL × 1 A1D9M 5-ethyl-1-[[3-[(3~{R})-4-ethyl-3-(2-hydroxyethyl)piperazin-1-yl]carbonyl-4-fluoranyl-phenyl]methyl]pyrimidine-2,4-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.10 Å R-free 0.241
9IM8 Mutated ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to a pyrimidine 2,4-diketone derivative inhibitor Deposited 2024-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 230–581（352 aa）
Mutation：T349S,L351R,S353G,P354L A1D9M 5-ethyl-1-[[3-[(3~{R})-4-ethyl-3-(2-hydroxyethyl)piperazin-1-yl]carbonyl-4-fluoranyl-phenyl]methyl]pyrimidine-2,4-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Resolution 2.10 Å R-free 0.241
9ZQ9 Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 1 Deposited 2025-12-18 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain P 90–212（123 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 Different construct Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain P 90–212（123 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 Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric
Chain P 90–583（494 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

29 other PDB entries and 49 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PARP2_HUMAN
Isoform —
PDB entities 9
Chains and sequence ranges Author chain P； PDBConstruct 1–494； UniProt 90–583

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9zqc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9zqc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9zqc
Deposition date deposition_date2025-12-18
Structure title titleNucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2
Keywords keywordsDNA damage binding protein, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier42.86 Å
Radius of gyration Rg (electron density) rg_electron41.18 Å
Forward intensity I(0) i01442790000.00
Molecular weight molecular_weight249150.0 kDa
Excluded volume excluded_volume285030 ų
Envelope volume envelope_volume414250 ų
Hydration-shell volume shell_volume80786 ų
Envelope diameter envelope_diameter140.5 Å
Shell Rg shell_rg49.02 Å
Envelope Rg envelope_rg40.55 Å
Shape Rg shape_rg41.09 Å
Total Rg total_rg41.69 Å
Total atoms total_atoms31669
Residues n_residues1674
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax131.7 Å
Rg (real space) rg_real42.58 Å
Rg uncertainty (real space) rg_real_error1.07 Å
I(0) (real space) i0_real1.4430e+09
I(0) uncertainty (real space) i0_real_error2.3560e+07
Rg (reciprocal space) rg_reciprocal42.86 Å
I(0) (reciprocal space) i0_reciprocal1443000000.0000
Solution quality estimate total_estimate0.8885
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary56.9 Å
Skewness Skewness skewness0.067
Kurtosis Kurtosis kurtosis-0.464
Angular range angular_range— – 0.1850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha88540000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.876
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

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8. Citations (1)

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9. Files and Curves (10)