SAXSdb — 4mn3

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

Chromobox protein homolog 7

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 7–62	Fragment：protein	peptide × 1 EDO 1,2-ETHANEDIOL × 3 MG MAGNESIUM ION × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；40% ethylene glycol, 0.1M HEPES pH 7.5, 5% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.54 Å R-free 0.213

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 4MN3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2K1B Solution NMR structure of the chromo domain of the chromobox protein homolog 7 Deposited 2008-02-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–62（56 aa） Fragment：Chromo domain: Residues 7-62	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 300；Pressure ambient NMR sample composition 10 mM phosphate, 300 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2L1B Solution NMR structure of the chromobox protein Cbx7 with H3K27me3 Deposited 2010-07-27	Different construct 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 8–62（55 aa） Fragment：UNP Residues 7-62	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 300；Pressure ambient NMR sample composition 0.5 mM [U-13C; U-15N] protein, 2.7 mM peptide, 10 mM sodium phosphate, 300 mM sodium chloride, 0.5 mM PMSF, 0.5 mM TCEP, 1 mM Benzamidine, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3GS2 Ring1B C-terminal domain/Cbx7 Cbox Complex Deposited 2009-03-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 219–248（30 aa） Fragment：Cbox domain, residues 219-248 Chain D 219–248（30 aa） Fragment：Cbox domain, residues 219-248	Not recorded	SO4 SULFATE ION × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；25% PEG MME 550, 0.1 M MES, 0.01 M zinc sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.70 Å R-free 0.243
3GS2 Ring1B C-terminal domain/Cbx7 Cbox Complex Deposited 2009-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 219–248（30 aa） Fragment：Cbox domain, residues 219-248	Not recorded	SO4 SULFATE ION × 2 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；25% PEG MME 550, 0.1 M MES, 0.01 M zinc sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.70 Å R-free 0.243
3GS2 Ring1B C-terminal domain/Cbx7 Cbox Complex Deposited 2009-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 219–248（30 aa） Fragment：Cbox domain, residues 219-248	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；25% PEG MME 550, 0.1 M MES, 0.01 M zinc sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.70 Å R-free 0.243
5EPJ Crystal Structure of chromodomain of CBX7 in complex with inhibitor UNC3866 Deposited 2015-11-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 7–62（56 aa）	Not recorded	UNX UNKNOWN LIGAND × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 3350, 0.2 M ammonium formate	Resolution 1.60 Å R-free 0.260
6V2R Crystal Structure of chromodomain of CBX7 mutant V13A in complex with inhibitor UNC3866 Deposited 2019-11-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 7–62（56 aa） Fragment：Chromodomain	Mutation：V13A	UNX UNKNOWN LIGAND × 17	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.5 M ammonium sulfate, 0.1 M bis-tris propane, pH 7	Resolution 1.60 Å R-free 0.235
8SII Crystal Structure of CBX7 with compound UNC4976 Deposited 2023-04-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 7–62（56 aa） Fragment：chromodomain	Not recorded	SO4 SULFATE ION × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.5 M Ammonium Sulfate, 0.1 M BIS-Tris propane PH7.0	Resolution 1.37 Å R-free 0.223
8SII Crystal Structure of CBX7 with compound UNC4976 Deposited 2023-04-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 7–62（56 aa） Fragment：chromodomain	Not recorded	SO4 SULFATE ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.5 M Ammonium Sulfate, 0.1 M BIS-Tris propane PH7.0	Resolution 1.37 Å R-free 0.223
9V9P Cryo-EM structure of the cPRC1-di-nucleosome (CBX7) complex Deposited 2025-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric	Chain S 1–251（251 aa） Chain Y 1–251（251 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.40 Å

7 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CBX7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–56； UniProt 7–62

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	4mn3
Deposition date deposition_date	2013-09-09
Structure title title	Chromodomain antagonists that target the polycomb-group methyllysine reader protein Chromobox homolog 7 (CBX7)
Keywords keywords	chromobox domain 7, TRANSCRIPTION REGULATOR; TRANSCRIPTION REGULATOR
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	12.84 Å
Radius of gyration Rg (electron density) rg_electron	11.48 Å
Forward intensity I(0) i0	1255670.00
Molecular weight molecular_weight	7891.0 kDa
Excluded volume excluded_volume	10108 Å³
Envelope volume envelope_volume	11306 Å³
Hydration-shell volume shell_volume	8588 Å³
Envelope diameter envelope_diameter	42.3 Å
Shell Rg shell_rg	16.85 Å
Envelope Rg envelope_rg	12.01 Å
Shape Rg shape_rg	11.42 Å
Total Rg total_rg	13.14 Å
Total atoms total_atoms	557
Residues n_residues	60
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	46.0 Å
Rg (real space) rg_real	12.77 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	1.2560e+06
I(0) uncertainty (real space) i0_real_error	1.7150e+04
Rg (reciprocal space) rg_reciprocal	12.78 Å
I(0) (reciprocal space) i0_reciprocal	1256000.0000
Solution quality estimate total_estimate	0.8400
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.7 Å
Skewness Skewness skewness	0.198
Kurtosis Kurtosis kurtosis	-0.239
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	347600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.652; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Chromobox protein homolog 7
Molecular weight formula_weight	6816.9 kDa
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	597

GEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE

来源 Source

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

Entity 2 Entity 2 polymer

Description description	peptide
Molecular weight formula_weight	681.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

XFAYKSX

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
Molecular weight formula_weight	326.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	40

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4mn3A00
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	63.290 Å
Unit-cell length b length_b	31.860 Å
Unit-cell length c length_c	38.390 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.02 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.542 Å
Low-resolution limit resolution_low	29.500 Å
R factor r_factor	0.1742
R_work r_work	0.1722
R_free r_free	0.2127

fit	/app/data/saxs_computation/mn/4mn3/4mn3.fit
pddf	/app/data/pr_computation/mn/4mn3/4mn3.pr.out
profile	/app/data/saxs_computation/mn/4mn3/4mn3.dat

Chromodomain antagonists that target the polycomb-group methyllysine reader protein Chromobox homolog 7 (CBX7)

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

Chromobox protein homolog 7

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)