SAXSdb — 1kna

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

HETEROCHROMATIN PROTEIN 1

Drosophila melanogaster

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 17–76	Fragment：Residues 23-76 Mutation：K38M	METHYLATED Histone H3 × 1 （P02299）	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

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 1KNA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KNE Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9 Deposited 2001-12-18	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–76（60 aa） Fragment：Residues 17-76	Mutation：K38M	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
1Q3L Chromodomain Of HP1 Complexed With Histone H3 Tail Containing monomethyllysine 9. Deposited 2003-07-30	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–76（60 aa） Fragment：sequence database residues 17-76	Not recorded	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 1.64 Å R-free 0.241
3P7J Drosophila HP1a chromo shadow domain Deposited 2010-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 131–206（76 aa） Fragment：UNP residues 131-206 Chain B 131–206（76 aa） Fragment：UNP residues 131-206	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；12% PEG400, 0.1 M HEPES. Cryoprotected in 12% PEG400, 0.1 M HEPES, 33% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.246
3P7J Drosophila HP1a chromo shadow domain Deposited 2010-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 131–206（76 aa） Fragment：UNP residues 131-206 Chain B 131–206（76 aa） Fragment：UNP residues 131-206	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；12% PEG400, 0.1 M HEPES. Cryoprotected in 12% PEG400, 0.1 M HEPES, 33% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.246
6ASZ Chromodomain HP1 with Y24F mutation bound to histone H3 peptide containing trimethyl lysine Deposited 2017-08-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–76（60 aa） Fragment：Chromo 1 domain, residues 17-76	Mutation：Y24F , K38M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.3；277 K；0.1 M MES, 3.4 M (NH4)2SO4	Resolution 1.52 Å R-free 0.274
6AT0 Chromodomain HP1 with a p-nitro-L-phenylalanine mutation at position 24 bound to histone H3 peptide containing trimethyl lysine Deposited 2017-08-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–76（60 aa） Fragment：Chromo 1 domain, residues 17-76	Mutation：K38M 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 5.8；277 K；0.1M MES, 3.0M (NH4)2SO4	Resolution 1.28 Å R-free 0.260
6MHA dHP1 Chromodomain Y24W variant bound to histone H3 peptide containing trimethyllysine Deposited 2018-09-17	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 22–74（53 aa）	Mutation：Y24W, K38M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；3.2 M Ammonium sulfate, 0.1 M MES	Resolution 1.50 Å R-free 0.219

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

View Construct and Data Evidence

UniProt name	HP1_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–69； UniProt 17–76

METHYLATED 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	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain P； UniProt 1–16	Fragment：Residues 1-16 Mutation：P16Y Non-standard monomer：Yes (specific site not provided by mmCIF)	HETEROCHROMATIN PROTEIN 1 × 1 （P05205）	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

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 1KNA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KNE Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9 Deposited 2001-12-18	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 1–16（16 aa） Fragment：Residues 1-16	Mutation：P16Y Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；283 K；Ammonium Sulfate, MES, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 283K	Resolution 2.40 Å R-free 0.267
2NQB Drosophila Nucleosome Structure Deposited 2006-10-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain A 1–135（135 aa） Chain E 1–135（135 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；Constituents of the crystallization buffer: Potassium Chloride, Manganese Chloride, and Potassium Cacodylate., pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.30 Å R-free 0.254
2PYO Drosophila nucleosome core Deposited 2007-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental 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 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 experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–20（19 aa） Fragment：N-TERMINAL TAIL, RESIDUES 2-19	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 100 MM SODIUM CITRATE, PH 5.4; 200 MM AMMONIUM ACETATE; 23% PEG 3350.	Resolution 2.55 Å R-free 0.222
4QLC Crystal structure of chromatosome at 3.5 angstrom resolution Deposited 2014-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain A 2–136（135 aa） Chain E 2–136（135 aa）	Not recorded	CIT CITRIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.75；291 K；0.1 mM Citric acid, 0.1mM potassium chloride, and 10% MPD, pH 3.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.50 Å R-free 0.243
4U68 Crystal structure of Rhino chromodomain in complex with H3K9me3 Deposited 2014-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 5–15（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；290 K；30 %(v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, 25 % (w/v) PEG 1500	Resolution 1.80 Å R-free 0.206
4U68 Crystal structure of Rhino chromodomain in complex with H3K9me3 Deposited 2014-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 5–15（11 aa） Chain F 5–15（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；290 K；30 %(v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, 25 % (w/v) PEG 1500	Resolution 1.80 Å R-free 0.206
4UUZ MCM2-histone complex Deposited 2014-08-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–136（136 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M HEPES PH7, 21% PEG3000	Resolution 2.90 Å R-free 0.230
4X23 CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE Deposited 2014-11-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain A 41–133（93 aa） Fragment：UNP RESIDUES 41-133 Chain E 41–133（93 aa） Fragment：UNP RESIDUES 41-133	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；10% MPD, 40MM SODIUM CACODYLATE, 24MM SPERMINE TETRA-HCL, 80MM SODIUM CHLORIDE, 20MM MAGNESIUM CHLORIDE; RESERVIOR 35% MPD. PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K	Resolution 3.50 Å R-free 0.286
4X23 CRYSTAL STRUCTURE OF CENP-C IN COMPLEX WITH THE NUCLEOSOME CORE PARTICLE Deposited 2014-11-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 41–133（93 aa） Fragment：UNP RESIDUES 41-133 Chain O 41–133（93 aa） Fragment：UNP RESIDUES 41-133	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；10% MPD, 40MM SODIUM CACODYLATE, 24MM SPERMINE TETRA-HCL, 80MM SODIUM CHLORIDE, 20MM MAGNESIUM CHLORIDE; RESERVIOR 35% MPD. PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K	Resolution 3.50 Å R-free 0.286
5WCU Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5 Deposited 2017-07-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain A 39–136（98 aa） Fragment：UNP residues 39-136 Chain E 39–136（98 aa） Fragment：UNP residues 39-136	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；291 K；0.1 M NH4NO3, 10% MPD (v/v)	Resolution 5.53 Å R-free 0.238
5WCU Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5 Deposited 2017-07-02	Different construct Different mutation/modification Different oligomeric state Different experimental 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain A 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain A 1–136（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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain A 1–136（136 aa） Chain E 1–136（136 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.07 Å
7VRF Crystal structure of Oxpecker chromodomain in complex with H3K9me3 Deposited 2021-10-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 5–15（11 aa） Chain D 5–15（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；0.2M ammonium citrate, 20% (w/v) PEG 3350	Resolution 1.70 Å R-free 0.238
7XYF Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome Deposited 2022-06-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric	Chain A 39–136（98 aa） Chain E 39–136（98 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7XYG Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome Deposited 2022-06-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric	Chain U 1–136（136 aa） Chain W 1–136（136 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；80 nM SWR1, 160 nM nucleosomes, 1 mM ADP, 10 mM NaF, 8 mM BeCl2, 0.05% glutaraldehyde, 20 mM HEPES-KOH pH 7.6, 1.5 mM MgCl2, 0.25 mM TCEP, 0.01% IGEPAL CA-630, 1% glycerol cryo-EM vitrification conditions Cryogen ETHANE；3 second blot time and blot force of 10.	Resolution 4.40 Å
9MU4 Structure of a native Drosophila melanogaster octameric nucleosome Deposited 2025-01-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain a 37–136（100 aa） Chain e 37–136（100 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
9MU5 Structure of a native Drosophila melanogaster hexameric nucleosome Deposited 2025-01-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: octameric	Chain a 45–136（92 aa） Chain e 45–136（92 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.30 Å
9MU9 Structure of a native Drosophila melanogaster Nucleosome Elongation Complex (Pol II EC-nucleosome). Composite map Deposited 2025-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain a 37–136（100 aa） Chain e 37–136（100 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；10 mM HEPES-HCl (pH = 7.5), 150 mM NaCl, 5% glycerol, 1 mM EDTA, 350 ug/mL 3x FLAG peptide, 1/1000th protease inhibitor cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.80 Å
9ZQ9 Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 1 Deposited 2025-12-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric	Chain E 1–136（136 aa） Chain F 1–136（136 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9ZQA Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 2 Deposited 2025-12-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric	Chain E 1–136（136 aa） Chain F 1–136（136 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.28 Å
9ZQB Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1 Deposited 2025-12-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric	Chain E 1–136（136 aa） Chain F 1–136（136 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.10 Å
9ZQC Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2 Deposited 2025-12-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 14-meric	Chain E 1–136（136 aa） Chain F 1–136（136 aa）	Mutation：C111S Mutation：C111S	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.37 Å

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

View Construct and Data Evidence

UniProt name	H3_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–16； UniProt 1–16

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1kna
Deposition date deposition_date	2001-12-18
Structure title title	Chromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9.
Keywords keywords	chromo, HP1, histone, dimethyllysine, methyllysine, H3, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	12.25 Å
Radius of gyration Rg (electron density) rg_electron	10.81 Å
Forward intensity I(0) i0	1196510.00
Molecular weight molecular_weight	7082.0 kDa
Excluded volume excluded_volume	8783 Å³
Envelope volume envelope_volume	9641 Å³
Hydration-shell volume shell_volume	7874 Å³
Envelope diameter envelope_diameter	34.1 Å
Shell Rg shell_rg	16.10 Å
Envelope Rg envelope_rg	11.14 Å
Shape Rg shape_rg	10.76 Å
Total Rg total_rg	12.31 Å
Total atoms total_atoms	499
Residues n_residues	57
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	37.0 Å
Rg (real space) rg_real	12.16 Å
Rg uncertainty (real space) rg_real_error	0.20 Å
I(0) (real space) i0_real	1.1970e+06
I(0) uncertainty (real space) i0_real_error	1.1120e+04
Rg (reciprocal space) rg_reciprocal	12.17 Å
I(0) (reciprocal space) i0_reciprocal	1197000.0000
Solution quality estimate total_estimate	0.9052
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.9 Å
Skewness Skewness skewness	0.081
Kurtosis Kurtosis kurtosis	-0.414
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	191400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.966

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	HETEROCHROMATIN PROTEIN 1
Molecular weight formula_weight	8586.5 kDa
Mutation mutation	K38M
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	585

MKKHHHHHHAEEEEEEYAVEKIIDRRVRKGMVEYYLKWKGYPETENTWEPENNLDCQDLIQQYEASRKD

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	fruit fly
NCBI Class编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	METHYLATED Histone H3
Molecular weight formula_weight	1756.0 kDa
Mutation mutation	P16Y
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

ARTKQTARKSTGGKAY

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	86

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1knaa_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.13 — Chromo domain-like
Family Family family	b.34.13.2 — Chromo domain

CATH v4.4 (1 domains)

Domain ID domain_id	1knaA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

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8. Citations (1)

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Unit-cell length a length_a	33.792 Å
Unit-cell length b length_b	76.883 Å
Unit-cell length c length_c	75.548 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	28.630 Å
R factor r_factor	—
R_work r_work	0.2280
R_free r_free	0.2590

fit	/app/data/saxs_computation/kn/1kna/1kna.fit
pddf	/app/data/pr_computation/kn/1kna/1kna.pr.out
profile	/app/data/saxs_computation/kn/1kna/1kna.dat

Chromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9.

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

HETEROCHROMATIN PROTEIN 1

State in the Current Structure

Other States of the Same Protein in the Database

METHYLATED Histone H3

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)