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9mu9

Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map

Method: ELECTRON MICROSCOPY Dmax: 209.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone H2A

OrganismNot specified

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 Other combination Heteromer Protein × 18 DNA 2 RNA 1 PDB declaration: 21-meric（21） Consistent with all polymer counts Chain c； UniProt 14–119 Chain g； UniProt 14–119 Not recorded RNA × 1 Template DNA × 1 Non-template DNA × 1 Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） 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

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 9MU9 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 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 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 oligomeric state Different ligand/ion 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 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
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 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 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 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 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 4
Chains and sequence ranges Author chain c； PDBConstruct 1–106； UniProt 14–119 Author chain g； PDBConstruct 1–106； UniProt 14–119

Histone H2B

OrganismNot specified

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 Other combination Heteromer Protein × 18 DNA 2 RNA 1 PDB declaration: 21-meric（21） Consistent with all polymer counts Chain d； UniProt 27–123 Chain h； UniProt 27–123 Not recorded RNA × 1 Template DNA × 1 Non-template DNA × 1 Histone H2A × 2 （P84051） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） 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

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 9MU9 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 construct Different oligomeric state 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 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 oligomeric state Different ligand/ion 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 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
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 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 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 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 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 5
Chains and sequence ranges Author chain d； PDBConstruct 1–97； UniProt 27–123 Author chain h； PDBConstruct 1–97； UniProt 27–123

Histone H3

OrganismNot specified

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 Other combination Heteromer Protein × 18 DNA 2 RNA 1 PDB declaration: 21-meric（21） Consistent with all polymer counts Chain a； UniProt 37–136 Chain e； UniProt 37–136 Not recorded RNA × 1 Template DNA × 1 Non-template DNA × 1 Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H4 × 2 （P84040） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） 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

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 9MU9 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 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 ligand/ion 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 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 1–135（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 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–20（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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 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 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 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 oligomeric state Different ligand/ion 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 oligomeric state Different ligand/ion 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 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
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 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 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 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 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 6
Chains and sequence ranges Author chain a； PDBConstruct 1–100； UniProt 37–136 Author chain e； PDBConstruct 1–100； UniProt 37–136

Histone H4

OrganismNot specified

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 Other combination Heteromer Protein × 18 DNA 2 RNA 1 PDB declaration: 21-meric（21） Consistent with all polymer counts Chain b； UniProt 24–103 Chain f； UniProt 24–103 Not recorded RNA × 1 Template DNA × 1 Non-template DNA × 1 Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） 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

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 9MU9 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 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 oligomeric state Different ligand/ion 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
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 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 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 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 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 7
Chains and sequence ranges Author chain b； PDBConstruct 1–80； UniProt 24–103 Author chain f； PDBConstruct 1–80； UniProt 24–103

DNA-directed RNA polymerase II subunit RPB1

OrganismNot specified

UniProt P04052

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 18 DNA 2 RNA 1 PDB declaration: 21-meric（21） Consistent with all polymer counts Chain A； UniProt 7–1476 Not recorded RNA × 1 Template DNA × 1 Non-template DNA × 1 Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） 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

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 9MU9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9MU7 Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain A 7–1476（1470 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 3.44 Å
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain A 7–1476（1470 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 3.37 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPB1_DROME
Isoform —
PDB entities 8
Chains and sequence ranges Author chain A； PDBConstruct 1–1470； UniProt 7–1476

DNA-directed RNA polymerase II subunit RPB2

OrganismNot specified

UniProt P08266

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 18 DNA 2 RNA 1 PDB declaration: 21-meric（21） Consistent with all polymer counts Chain B； UniProt 13–1176 Not recorded RNA × 1 Template DNA × 1 Non-template DNA × 1 Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） 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

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 9MU9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9MU7 Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain B 13–1176（1164 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 3.44 Å
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain B 13–1176（1164 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 3.37 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPB2_DROME
Isoform —
PDB entities 9
Chains and sequence ranges Author chain B； PDBConstruct 1–1164； UniProt 13–1176

DNA-directed RNA polymerase II subunit RPB3

OrganismNot specified

UniProt O97183

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 18 DNA 2 RNA 1 PDB declaration: 21-meric（21） Consistent with all polymer counts Chain C； UniProt 2–270 Not recorded RNA × 1 Template DNA × 1 Non-template DNA × 1 Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） 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

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 9MU9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9MU7 Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain C 2–270（269 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 3.44 Å
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain C 2–270（269 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 3.37 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name O97183_DROME
Isoform —
PDB entities 10
Chains and sequence ranges Author chain C； PDBConstruct 1–269； UniProt 2–270

DNA-directed RNA polymerases I, II, and III subunit RPABC2

OrganismNot specified

UniProt Q24320

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 18 DNA 2 RNA 1 PDB declaration: 21-meric（21） Consistent with all polymer counts Chain F； UniProt 47–130 Not recorded RNA × 1 Template DNA × 1 Non-template DNA × 1 Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） 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

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 9MU9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9MU7 Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain F 47–130（84 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 3.44 Å
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain F 47–130（84 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 3.37 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPAB2_DROME
Isoform —
PDB entities 11
Chains and sequence ranges Author chain F； PDBConstruct 1–84； UniProt 47–130

DNA-directed RNA polymerases I, II, and III subunit RPABC3

OrganismNot specified

UniProt Q9VNZ3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 18 DNA 2 RNA 1 PDB declaration: 21-meric（21） Consistent with all polymer counts Chain H； UniProt 2–148 Not recorded RNA × 1 Template DNA × 1 Non-template DNA × 1 Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） 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

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 9MU9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9MU7 Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain H 2–148（147 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 3.44 Å
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain H 2–148（147 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 3.37 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9VNZ3_DROME
Isoform —
PDB entities 12
Chains and sequence ranges Author chain H； PDBConstruct 1–147； UniProt 2–148

DNA-directed RNA polymerase II subunit RPB9

OrganismNot specified

UniProt P36958

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 18 DNA 2 RNA 1 PDB declaration: 21-meric（21） Consistent with all polymer counts Chain I； UniProt 14–129 Not recorded RNA × 1 Template DNA × 1 Non-template DNA × 1 Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） 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

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 9MU9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9MU7 Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain I 14–129（116 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 3.44 Å
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain I 14–129（116 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 3.37 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPB9_DROME
Isoform —
PDB entities 13
Chains and sequence ranges Author chain I； PDBConstruct 1–116； UniProt 14–129

DNA-directed RNA polymerases I, II, and III subunit RPABC5

OrganismNot specified

UniProt Q9VC49

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 18 DNA 2 RNA 1 PDB declaration: 21-meric（21） Consistent with all polymer counts Chain J； UniProt 1–67 Not recorded RNA × 1 Template DNA × 1 Non-template DNA × 1 Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） 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

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 9MU9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9MU7 Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain J 1–67（67 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 3.44 Å
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain J 1–67（67 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 3.37 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPAB5_DROME
Isoform —
PDB entities 14
Chains and sequence ranges Author chain J； PDBConstruct 1–67； UniProt 1–67

DNA-directed RNA polymerase II subunit RPB11

OrganismNot specified

UniProt Q9VJE4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 18 DNA 2 RNA 1 PDB declaration: 21-meric（21） Consistent with all polymer counts Chain K； UniProt 1–116 Not recorded RNA × 1 Template DNA × 1 Non-template DNA × 1 Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） 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

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 9MU9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9MU7 Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain K 1–116（116 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 3.44 Å
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain K 1–116（116 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 3.37 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPB11_DROME
Isoform —
PDB entities 15
Chains and sequence ranges Author chain K； PDBConstruct 1–116； UniProt 1–116

DNA-directed RNA polymerase II subunit RPB12

OrganismNot specified

UniProt Q6IGE3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 18 DNA 2 RNA 1 PDB declaration: 21-meric（21） Consistent with all polymer counts Chain L； UniProt 12–57 Not recorded RNA × 1 Template DNA × 1 Non-template DNA × 1 Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB5 × 1 （Q7JZF5） 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

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 9MU9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9MU7 Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain L 12–57（46 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 3.44 Å
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain L 12–57（46 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 3.37 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q6IGE3_DROME
Isoform —
PDB entities 16
Chains and sequence ranges Author chain L； PDBConstruct 1–46； UniProt 12–57

DNA-directed RNA polymerase II subunit RPB5

OrganismNot specified

UniProt Q7JZF5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 18 DNA 2 RNA 1 PDB declaration: 21-meric（21） Consistent with all polymer counts Chain E； UniProt 1–210 Not recorded RNA × 1 Template DNA × 1 Non-template DNA × 1 Histone H2A × 2 （P84051） Histone H2B × 2 （P02283） Histone H3 × 2 （P02299） Histone H4 × 2 （P84040） DNA-directed RNA polymerase II subunit RPB1 × 1 （P04052） DNA-directed RNA polymerase II subunit RPB2 × 1 （P08266） DNA-directed RNA polymerase II subunit RPB3 × 1 （O97183） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （Q24320） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （Q9VNZ3） DNA-directed RNA polymerase II subunit RPB9 × 1 （P36958） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q9VC49） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q9VJE4） DNA-directed RNA polymerase II subunit RPB12 × 1 （Q6IGE3） 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

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 9MU9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9MU7 Structure of a native Drosophila melanogaster Pol II Elongation Complex with a well-defined Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain E 1–210（210 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 3.44 Å
9MU8 Structure of a native Drosophila melanogaster Pol II Elongation Complex without Rpb4/Rpb7 stalk Deposited 2025-01-13 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: tridecameric
Chain E 1–210（210 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 3.37 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q7JZF5_DROME
Isoform —
PDB entities 17
Chains and sequence ranges Author chain E； PDBConstruct 1–210； UniProt 1–210

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 9mu9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9mu9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9mu9
Deposition date deposition_date2025-01-13
最后修订 last_revision2025-02-19
Structure title titleStructure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map
Keywords keywordspolymerase, Pol II, transcription, mRNA; TRANSCRIPTION
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier70.52 Å
Radius of gyration Rg (electron density) rg_electron68.82 Å
Forward intensity I(0) i06653010000.00
Molecular weight molecular_weight611200.0 kDa
Excluded volume excluded_volume733290 ų
Envelope volume envelope_volume1152700 ų
Hydration-shell volume shell_volume145980 ų
Envelope diameter envelope_diameter240.2 Å
Shell Rg shell_rg64.85 Å
Envelope Rg envelope_rg67.36 Å
Shape Rg shape_rg68.73 Å
Total Rg total_rg69.03 Å
Total atoms total_atoms42423
Residues n_residues4793
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 dmax209.9 Å
Rg (real space) rg_real70.46 Å
Rg uncertainty (real space) rg_real_error1.21 Å
I(0) (real space) i0_real6.6350e+09
I(0) uncertainty (real space) i0_real_error1.2750e+08
Rg (reciprocal space) rg_reciprocal69.24 Å
I(0) (reciprocal space) i0_reciprocal6632000000.0000
Solution quality estimate total_estimate0.5941
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary66.8 Å
Skewness Skewness skewness0.484
Kurtosis Kurtosis kurtosis-0.529
Angular range angular_range— – 0.1100 Å−1
Current regularization parameter α current_alpha0.0237
Highest regularization parameter α highest_alpha577400000.0000
Real-space data points n_real_points23
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.898; Stabil: 0.999; Sysdev: 0.006; Positv: 1.000; Valcen: 0.993; Smooth: 0.011
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (18)

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8. Citations (1)

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9. Files and Curves (10)