SAXSdb — 6hw2

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

Chromobox protein homolog 3

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 109–183 Chain C； UniProt 109–183	Not recorded	Voltage-dependent L-type calcium channel subunit beta-4 × 1 CA CALCIUM ION × 4 GOL GLYCEROL × 1 BME BETA-MERCAPTOETHANOL × 5 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；292 K；0.15 M NaCl, 12-14% PEG 3350 , pH 5.0, calcium acetate, VAPOR DIFFUSION, temperature 292K	Resolution 1.94 Å R-free 0.209

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 6HW2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2L11 Solution NMR structure of the Cbx3 in complex with H3K9me3 peptide Deposited 2010-07-22	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 × 2 PDB declaration: dimeric	Chain A 29–81（53 aa） Fragment：UNP Residues 29-81	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 200；Pressure ambient NMR sample composition 20 mM sodium phosphate, 200 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.5 mM PMSF, 1 mM Benzamidine, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3DM1 Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide Deposited 2008-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 29–86（58 aa） Fragment：Chromo 1 domain: Residues 29-86	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267
3DM1 Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide Deposited 2008-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 29–86（58 aa） Fragment：Chromo 1 domain: Residues 29-86	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267
3DM1 Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide Deposited 2008-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 29–86（58 aa） Fragment：Chromo 1 domain: Residues 29-86	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267
3DM1 Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide Deposited 2008-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 29–86（58 aa） Fragment：Chromo 1 domain: Residues 29-86	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267
3DM1 Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide Deposited 2008-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 29–86（58 aa） Fragment：Chromo 1 domain: Residues 29-86 Chain C 29–86（58 aa） Fragment：Chromo 1 domain: Residues 29-86 Chain E 29–86（58 aa） Fragment：Chromo 1 domain: Residues 29-86 Chain G 29–86（58 aa） Fragment：Chromo 1 domain: Residues 29-86	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267
3KUP Crystal Structure of the CBX3 Chromo Shadow Domain Deposited 2009-11-27	Different construct 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 110–173（64 aa） Fragment：Chromo Shadow Domain (UNP residues 110-173) Chain B 110–173（64 aa） Fragment：Chromo Shadow Domain (UNP residues 110-173)	Not recorded	UNX UNKNOWN LIGAND × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；30% PEG1500, 0.2M sodium chloride, 0.1M HEPES, 5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.77 Å R-free 0.261
3KUP Crystal Structure of the CBX3 Chromo Shadow Domain Deposited 2009-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 110–173（64 aa） Fragment：Chromo Shadow Domain (UNP residues 110-173) Chain D 110–173（64 aa） Fragment：Chromo Shadow Domain (UNP residues 110-173)	Not recorded	UNX UNKNOWN LIGAND × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；30% PEG1500, 0.2M sodium chloride, 0.1M HEPES, 5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.77 Å R-free 0.261
3TZD Crystal structure of the complex of Human Chromobox Homolog 3 (CBX3) Deposited 2011-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 29–81（53 aa） Fragment：UNP residues 29-81	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；peg, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K	Resolution 1.81 Å R-free 0.231
5T1I CBX3 chromo shadow domain in complex with histone H3 peptide Deposited 2016-08-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 110–176（67 aa） Fragment：unp residues 110-176 Chain B 110–176（67 aa） Fragment：unp residues 110-176	Not recorded	UNX UNKNOWN LIGAND × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG 3350, 0.2 M sodium chloride, 0.1 M Hepes, 5% Ethylene Glycol	Resolution 1.60 Å R-free 0.239
9OSC Crystal structure of HP1gamma chromoshadow domain in complex with KAP1 peptide Deposited 2025-05-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 110–176（67 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.0 M LiCl2, 0.1 M citrate buffer pH 4.0, and 20% PEG6000	Resolution 1.77 Å R-free 0.236

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CBX3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–75； UniProt 109–183 Author chain C； PDBConstruct 1–75； UniProt 109–183

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	6hw2
Deposition date deposition_date	2018-10-11
Structure title title	The Crystal Structure of CaV beta4c in complex with HP1gamma chromo shadow domains
Keywords keywords	Complex, transport protein; TRANSPORT 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	23.19 Å
Radius of gyration Rg (electron density) rg_electron	22.05 Å
Forward intensity I(0) i0	15837400.00
Molecular weight molecular_weight	29745.0 kDa
Excluded volume excluded_volume	37150 Å³
Envelope volume envelope_volume	47077 Å³
Hydration-shell volume shell_volume	18816 Å³
Envelope diameter envelope_diameter	86.6 Å
Shell Rg shell_rg	27.62 Å
Envelope Rg envelope_rg	22.89 Å
Shape Rg shape_rg	22.04 Å
Total Rg total_rg	22.87 Å
Total atoms total_atoms	4112
Residues n_residues	259
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	82.8 Å
Rg (real space) rg_real	23.30 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	1.5840e+07
I(0) uncertainty (real space) i0_real_error	2.5120e+05
Rg (reciprocal space) rg_reciprocal	23.28 Å
I(0) (reciprocal space) i0_reciprocal	15840000.0000
Solution quality estimate total_estimate	0.8463
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.499
Kurtosis Kurtosis kurtosis	-0.073
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3107000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.736; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.841; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Voltage-dependent L-type calcium channel subunit beta-4
Molecular weight formula_weight	17531.8 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	4353

GSRPSDSDVSLEEDREAIRQEREQQAAIQLERAKSKPVAFAVKTNVSYCGALDEDVPVPSTAISFDAKDFLHIKEKYNNDWWIGRLVKEGCEIGFIPSPLRLENIRIQQEQKRGRFHGEFAKQKQKVTEHIPPYDVVPSMRPVVLVGPSLKGYE

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	Chromobox protein homolog 3
Molecular weight formula_weight	8468.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C

DAADKPRGFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLTWHSCPEDEAQ

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 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	202

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6hw2b_
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

Domain ID domain_id	d6hw2c_
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 (3 domains)

Domain ID domain_id	6hw2A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	6hw2B00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6hw2C00
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	115.026 Å
Unit-cell length b length_b	58.036 Å
Unit-cell length c length_c	57.546 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.70 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.941 Å
Low-resolution limit resolution_low	33.120 Å
R factor r_factor	0.1792
R_work r_work	0.1775
R_free r_free	0.2095

fit	/app/data/saxs_computation/hw/6hw2/6hw2.fit
pddf	/app/data/pr_computation/hw/6hw2/6hw2.pr.out
profile	/app/data/saxs_computation/hw/6hw2/6hw2.dat

The Crystal Structure of CaV beta4c in complex with HP1gamma chromo shadow domains

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

Chromobox protein homolog 3

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)