← Back to search
4qlc

Crystal structure of chromatosome at 3.5 angstrom resolution

Method: X-RAY DIFFRACTION Dmax: 138.6 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

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 × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts Chain A； UniProt 2–136 Chain E； UniProt 2–136 Not recorded DNA (167-mer) × 1 DNA (167-mer) × 1 Histone H4 × 2 （P84040） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） H5 × 1 （P02259） 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

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 4QLC 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–135（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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 2–136（135 aa）
Chain E 2–136（135 aa）
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 ligand/ion 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 ligand/ion 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
4U68 Crystal structure of Rhino chromodomain in complex with H3K9me3 Deposited 2014-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain A 39–136（98 aa） 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 ligand/ion 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain A 1–136（136 aa）
Chain E 1–136（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
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 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 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 construct 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 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 ligand/ion 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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
9ZQC Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2 Deposited 2025-12-18 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 × 11 PDB declaration: 14-meric
Chain E 1–136（136 aa）
Chain F 1–136（136 aa）
Mutation：C111S Mutation：C111S No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.37 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 A； PDBConstruct 1–135； UniProt 2–136 Author chain E； PDBConstruct 1–135； UniProt 2–136

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 × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts Chain B； UniProt 2–103 Chain F； UniProt 2–103 Not recorded DNA (167-mer) × 1 DNA (167-mer) × 1 Histone H3 × 2 （P02299） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） H5 × 1 （P02259） 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

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 4QLC 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 ligand/ion 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 oligomeric state Different ligand/ion 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 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 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
4UUZ MCM2-histone complex Deposited 2014-08-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental method 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 7.4
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 ligand/ion Different experimental method 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 construct Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 method 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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
9ZQC Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2 Deposited 2025-12-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 2.37 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 B； PDBConstruct 1–102； UniProt 2–103 Author chain F； PDBConstruct 1–102； UniProt 2–103

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 × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts Chain C； UniProt 2–124 Chain G； UniProt 2–124 Not recorded DNA (167-mer) × 1 DNA (167-mer) × 1 Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） Histone H2B × 2 （P02283） H5 × 1 （P02259） 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

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 4QLC 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 ligand/ion 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 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
4X23 CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE Deposited 2014-11-25 Different construct Different oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å
6PWE Cryo-EM structure of nucleosome core particle Deposited 2019-07-22 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 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 construct 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 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 ligand/ion 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 method 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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
9ZQC Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2 Deposited 2025-12-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 2.37 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 5
Chains and sequence ranges Author chain C； PDBConstruct 1–123； UniProt 2–124 Author chain G； PDBConstruct 1–123； UniProt 2–124

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 × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts Chain D； UniProt 2–123 Chain H； UniProt 2–123 Not recorded DNA (167-mer) × 1 DNA (167-mer) × 1 Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） Histone H2A × 2 （P84051） H5 × 1 （P02259） 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

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 4QLC 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 ligand/ion 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 oligomeric state Different ligand/ion 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
4X23 CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE Deposited 2014-11-25 Different construct Different oligomeric state Different ligand/ion 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 ligand/ion 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 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 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 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 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 construct 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 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 ligand/ion 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 ligand/ion Different experimental method 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 construct Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 method 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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
9ZQC Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2 Deposited 2025-12-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 2.37 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 6
Chains and sequence ranges Author chain D； PDBConstruct 1–122； UniProt 2–123 Author chain H； PDBConstruct 1–122； UniProt 2–123

H5

Gallus gallus

UniProt P02259

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 × 9 DNA 2 PDB declaration: undecameric（11） Consistent with all polymer counts Chain U； UniProt 23–99 Not recorded DNA (167-mer) × 1 DNA (167-mer) × 1 Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） 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

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 4QLC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1HST CRYSTAL STRUCTURE OF GLOBULAR DOMAIN OF HISTONE H5 AND ITS IMPLICATIONS FOR NUCLEOSOME BINDING Deposited 1993-03-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–108（90 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å
1HST CRYSTAL STRUCTURE OF GLOBULAR DOMAIN OF HISTONE H5 AND ITS IMPLICATIONS FOR NUCLEOSOME BINDING Deposited 1993-03-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 19–108（90 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å
5WCU Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5 Deposited 2017-07-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain U 23–98（76 aa） Fragment：UNP residues 23-98
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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain V 23–98（76 aa） Fragment：UNP residues 23-98
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
7C0J Crystal structure of chimeric mutant of GH5 in complex with Z-DNA Deposited 2020-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 25–64（40 aa）
Chain A 76–88（13 aa）
Chain A 92–93（2 aa）
Chain A 95–98（4 aa）
Chain B 25–64（40 aa）
Chain B 76–88（13 aa）
Chain B 92–93（2 aa）
Chain B 95–98（4 aa）
Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A Mutation：K41G,S42E,R43G,K53A,R95A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；MES pH 6.0, PEG 4000, ethylene glycol
Resolution 2.75 Å R-free 0.248
7XVM Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment) Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain U 2–190（189 aa）
Chain V 2–190（189 aa）
Not recorded CA CALCIUM ION × 18 CL CHLORIDE ION × 3 K POTASSIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5)
Resolution 2.84 Å R-free 0.259
8XJV Structural basis for the linker histone H5-nucleosome binding and chromatin compaction Deposited 2023-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 108 PDB declaration: 110-meric
Chain Ah 1–190（190 aa）
Chain Ai 1–190（190 aa）
Chain Aj 1–190（190 aa）
Chain Ak 1–190（190 aa）
Chain Al 1–190（190 aa）
Chain Am 1–190（190 aa）
Chain An 1–190（190 aa）
Chain Ao 1–190（190 aa）
Chain Ap 1–190（190 aa）
Chain Aq 1–190（190 aa）
Chain Ar 1–190（190 aa）
Chain As 1–190（190 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.60 Å

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H5_CHICK
Isoform —
PDB entities 7
Chains and sequence ranges Author chain U； PDBConstruct 1–77； UniProt 23–99

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 4qlc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4qlc
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id4qlc
Deposition date deposition_date2014-06-11
Structure title titleCrystal structure of chromatosome at 3.5 angstrom resolution
Keywords keywords;NUCLEOSOME CORE PARTICLE, HISTONE FOLD, CHROMOSOME, CHROMATIN, Global histone H5, gH5, NCP167, Regulation, SEGREGATION, CHROMATOSOME, gH1, Liker Histone H5, Linker DNA, Protein-DNA Complexes, DNA BINDING PROTEIN-DNA complex, CHROMATIN BINDING PROTEIN-DNA complex ;; CHROMATIN BINDING PROTEIN/DNA
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier43.12 Å
Radius of gyration Rg (electron density) rg_electron40.67 Å
Forward intensity I(0) i01041980000.00
Molecular weight molecular_weight195970.0 kDa
Excluded volume excluded_volume216200 ų
Envelope volume envelope_volume334420 ų
Hydration-shell volume shell_volume67408 ų
Envelope diameter envelope_diameter138.8 Å
Shell Rg shell_rg47.28 Å
Envelope Rg envelope_rg40.24 Å
Shape Rg shape_rg40.51 Å
Total Rg total_rg41.26 Å
Total atoms total_atoms13355
Residues n_residues1157
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax138.6 Å
Rg (real space) rg_real42.98 Å
Rg uncertainty (real space) rg_real_error1.19 Å
I(0) (real space) i0_real1.0420e+09
I(0) uncertainty (real space) i0_real_error1.7830e+07
Rg (reciprocal space) rg_reciprocal43.12 Å
I(0) (reciprocal space) i0_reciprocal1042000000.0000
Solution quality estimate total_estimate0.8266
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.7 Å
Skewness Skewness skewness0.177
Kurtosis Kurtosis kurtosis-0.556
Angular range angular_range— – 0.1850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha83260000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (8)

▼

7. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id4qlcA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id4qlcB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id4qlcC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id4qlcD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id4qlcE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id4qlcF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id4qlcG00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id4qlcH00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology20 — Histone, subunit A
Homologous superfamily homologous superfamily10 — Histone, subunit A
Domain ID domain_id4qlcU00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
▶

8. Citations (1)

▶

9. Files and Curves (10)