SAXSdb — 9cea

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

Chromobox protein homolog 5

Homo sapiens

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 113–175 Chain B； UniProt 113–175	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES pH 7, 0.2 M sodium chloride and 20% w/v PEG6000	Resolution 2.15 Å R-free 0.277
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 113–175 Chain D； UniProt 113–175	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES pH 7, 0.2 M sodium chloride and 20% w/v PEG6000	Resolution 2.15 Å R-free 0.277

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 9CEA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3FDT Crystal structure of the complex of human chromobox homolog 5 (CBX5) with H3K9(me)3 peptide Deposited 2008-11-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 18–75（58 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；35% PEG 400, 0.2M Na Cl, 0.1M Tris (pH 8.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.257
3I3C Crystal Structural of CBX5 Chromo Shadow Domain Deposited 2009-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–173（64 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；20% PEG3350, 0.2M di-Na Tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP	Resolution 2.48 Å R-free 0.303
3I3C Crystal Structural of CBX5 Chromo Shadow Domain Deposited 2009-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 110–173（64 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；20% PEG3350, 0.2M di-Na Tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP	Resolution 2.48 Å R-free 0.303
3I3C Crystal Structural of CBX5 Chromo Shadow Domain Deposited 2009-06-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 110–173（64 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；20% PEG3350, 0.2M di-Na Tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP	Resolution 2.48 Å R-free 0.303
3I3C Crystal Structural of CBX5 Chromo Shadow Domain Deposited 2009-06-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 110–173（64 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；20% PEG3350, 0.2M di-Na Tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP	Resolution 2.48 Å R-free 0.303
8UXQ Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome Deposited 2023-11-09	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric	Chain A 2–191（190 aa） Chain C 2–191（190 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.30 Å
9CDW Crystal structure of HP1alpha chromoshadow domain in complex with KAP1 peptide Deposited 2024-06-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 111–174（64 aa） Chain C 111–174（64 aa）	Not recorded	PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Bis-Tris pH 5.8, 0.2 M MgCl2, 20% PEG3350, 30 mM glycyl-glycyl-glycine	Resolution 2.40 Å R-free 0.252
9CDW Crystal structure of HP1alpha chromoshadow domain in complex with KAP1 peptide Deposited 2024-06-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 111–174（64 aa） Chain D 111–174（64 aa）	Not recorded	PGE TRIETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Bis-Tris pH 5.8, 0.2 M MgCl2, 20% PEG3350, 30 mM glycyl-glycyl-glycine	Resolution 2.40 Å R-free 0.252
9CMT The crystal structure of HP1alpha CSD-Agno complex Deposited 2024-07-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 112–176（65 aa） Chain B 112–176（65 aa） Chain D 112–176（65 aa） Chain E 112–176（65 aa）	Mutation：C133S, T145S Mutation：C133S, T145S Mutation：C133S, T145S Mutation：C133S, T145S	F6Z 3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-5-CARBOXYLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1 uL protein solution (about 10 mg/ml) and 1 uL reservoir solution containing 0.01 M NiCl2, 0.1 M Tris-HCl, pH 8.5, and 20% PEG2000MME (v/v)	Resolution 3.17 Å R-free 0.286

5 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CBX5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–63； UniProt 113–175 Author chain B； PDBConstruct 1–63； UniProt 113–175 Author chain C； PDBConstruct 1–63； UniProt 113–175 Author chain D； PDBConstruct 1–63； UniProt 113–175

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	9cea
Deposition date deposition_date	2024-06-26
最后修订 last_revision	2025-06-11
Structure title title	Crystal structure of HP1alpha chromoshadow domain
Keywords keywords	HP1a, CSD domain, TRANSCRIPTION; TRANSCRIPTION
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	23.10 Å
Radius of gyration Rg (electron density) rg_electron	22.24 Å
Forward intensity I(0) i0	12275000.00
Molecular weight molecular_weight	26740.0 kDa
Excluded volume excluded_volume	33632 Å³
Envelope volume envelope_volume	42401 Å³
Hydration-shell volume shell_volume	17119 Å³
Envelope diameter envelope_diameter	79.1 Å
Shell Rg shell_rg	27.53 Å
Envelope Rg envelope_rg	22.39 Å
Shape Rg shape_rg	22.23 Å
Total Rg total_rg	23.04 Å
Total atoms total_atoms	1876
Residues n_residues	243
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	79.2 Å
Rg (real space) rg_real	23.21 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	1.2280e+07
I(0) uncertainty (real space) i0_real_error	1.7240e+05
Rg (reciprocal space) rg_reciprocal	23.18 Å
I(0) (reciprocal space) i0_reciprocal	12270000.0000
Solution quality estimate total_estimate	0.8717
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.408
Kurtosis Kurtosis kurtosis	-0.348
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2389000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.814; Smooth: 0.954

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	63.758 Å
Unit-cell length b length_b	66.854 Å
Unit-cell length c length_c	70.908 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	46.180 Å
R factor r_factor	0.2298
R_work r_work	0.2273
R_free r_free	0.2773

Description description	Chromobox protein homolog 5
Molecular weight formula_weight	7222.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	1991

Crystal structure of HP1alpha chromoshadow domain

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

Chromobox protein homolog 5

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	107

fit	/app/data/saxs_computation/ce/9cea/9cea.fit
pddf	/app/data/pr_computation/ce/9cea/9cea.pr.out
profile	/app/data/saxs_computation/ce/9cea/9cea.dat