SAXSdb — 3i3c

▼

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 110–173	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 110–173	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 110–173	Not recorded	No other associated polymer	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 110–173	Not recorded	No other associated polymer	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

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 3I3C	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 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
8UXQ Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome Deposited 2023-11-09	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: 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 mutation/modification 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 mutation/modification 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
9CEA Crystal structure of HP1alpha chromoshadow domain Deposited 2024-06-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 113–175（63 aa） Chain B 113–175（63 aa）	Not recorded	No recorded non-water small molecule	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
9CEA Crystal structure of HP1alpha chromoshadow domain Deposited 2024-06-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 113–175（63 aa） Chain D 113–175（63 aa）	Not recorded	No recorded non-water small molecule	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
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 7 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 12–75； UniProt 110–173 Author chain B； PDBConstruct 12–75； UniProt 110–173 Author chain C； PDBConstruct 12–75； UniProt 110–173 Author chain D； PDBConstruct 12–75； UniProt 110–173

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3i3c
Deposition date deposition_date	2009-06-30
Structure title title	Crystal Structural of CBX5 Chromo Shadow Domain
Keywords keywords	;CBX5, Chromo Shadow Domain, Structural Genomics, Structural Genomics Consortium, SGC, Centromere, Nucleus, Phosphoprotein, TRANSCRIPTION ;; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	24.30 Å
Radius of gyration Rg (electron density) rg_electron	23.52 Å
Forward intensity I(0) i0	10883200.00
Molecular weight molecular_weight	25107.0 kDa
Excluded volume excluded_volume	31585 Å³
Envelope volume envelope_volume	42386 Å³
Hydration-shell volume shell_volume	16386 Å³
Envelope diameter envelope_diameter	76.8 Å
Shell Rg shell_rg	28.47 Å
Envelope Rg envelope_rg	23.17 Å
Shape Rg shape_rg	23.53 Å
Total Rg total_rg	24.24 Å
Total atoms total_atoms	1764
Residues n_residues	229
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

▼

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

Maximum dimension Dmax dmax	77.2 Å
Rg (real space) rg_real	24.51 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.0880e+07
I(0) uncertainty (real space) i0_real_error	1.4600e+05
Rg (reciprocal space) rg_reciprocal	24.46 Å
I(0) (reciprocal space) i0_reciprocal	10880000.0000
Solution quality estimate total_estimate	0.8321
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	19.6 Å
Skewness Skewness skewness	0.376
Kurtosis Kurtosis kurtosis	-0.799
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3090000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.753; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.630; Smooth: 0.925

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Chromobox protein homolog 5
Molecular weight formula_weight	8454.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	1817

SSGRENLYFQGSNDIARGFERGLEPEKIIGATDSCGDLMFLMKWKDTDEADLVLAKEANVKCPQIVIAFYEERLT

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 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	35

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3i3ca_
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	d3i3cb_
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	d3i3cc_
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	d3i3cd_
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 (4 domains)

Domain ID domain_id	3i3cA00
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	3i3cB00
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	3i3cC00
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	3i3cD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	81.660 Å
Unit-cell length b length_b	126.587 Å
Unit-cell length c length_c	31.399 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.480 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2680
R_work r_work	0.2660
R_free r_free	0.3030

fit	/app/data/saxs_computation/i3/3i3c/3i3c.fit
pddf	/app/data/pr_computation/i3/3i3c/3i3c.pr.out
profile	/app/data/saxs_computation/i3/3i3c/3i3c.dat

Crystal Structural of CBX5 Chromo Shadow 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