SAXSdb — 9cmt

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Agnoprotein × 2 （P03086） ;3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-5-CARBOXYLIC ACID ; × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CBX5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–65； UniProt 112–176 Author chain B； PDBConstruct 1–65； UniProt 112–176 Author chain D； PDBConstruct 1–65； UniProt 112–176 Author chain E； PDBConstruct 1–65； UniProt 112–176

Agnoprotein

OrganismNot specified

UniProt P03086

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Chromobox protein homolog 5 × 4 （P45973） ;3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-5-CARBOXYLIC ACID ; × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AGNO_POVJC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–16； UniProt 4–19 Author chain F； PDBConstruct 1–16； UniProt 4–19

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	9cmt
Deposition date deposition_date	2024-07-15
Last revision last_revision	2025-05-28
Structure title title	The crystal structure of HP1alpha CSD-Agno complex
Keywords keywords	heterochromatin protein 1 alpha, Agnoprotein, JC polyomavirus, dimerization, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9cmt__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9cmt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9cmt__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	25.13 Å
Rg (electron density)	24.37 Å
Total Rg	25.21 Å
Atom count	2369
Residues	290
Excluded volume	42319 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9cmt__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Chromobox protein homolog 5
Molecular weight formula_weight	7392.4 kDa
Mutation mutation	C133S, T145S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E
Atom count atom_count	2369

EIARGFERGLEPEKIIGATDSSGDLMFLMKWKDSDEADLVLAKEANVKCPQIVIAFYEERLTWHA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	Agnoprotein
Molecular weight formula_weight	1866.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

RQLSRKASVKVSKTWS

Entity 3 Entity 3 non-polymer

Description description	;3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-5-CARBOXYLIC ACID ;
Molecular weight formula_weight	376.3 kDa
Source method src_method	syn
Copy count entity_count	2

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Unit-cell length a length_a	112.961 Å
Unit-cell length b length_b	112.961 Å
Unit-cell length c length_c	154.687 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	32

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	tetragonal

Resolution resolution	3.170 Å
Low-resolution limit resolution_low	29.840 Å
R factor r_factor	0.2518
R_work r_work	0.2479
R_free r_free	0.2861

The crystal structure of HP1alpha CSD-Agno complex

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

Agnoprotein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9cmt__assembly_1__model_1

9cmt__assembly_1__model_1 | I(q)

9cmt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

7. Citations (1)

The crystal structure of HP1alpha CSD-Agno complex

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Agnoprotein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9cmt__assembly_1__model_1

9cmt__assembly_1__model_1 | I(q)

9cmt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

7. Citations (1)