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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 112–176 Chain B； UniProt 112–176 Chain D； UniProt 112–176 Chain E； UniProt 112–176	Mutation：C133S, T145S	Agnoprotein × 2 （P03086） 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

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 9CMT	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 ligand/ion 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 ligand/ion 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 ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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

5 other PDB entries and 10 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 1–65； 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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain C； UniProt 4–19 Chain F； UniProt 4–19	Not recorded	Chromobox protein homolog 5 × 4 （P45973） 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

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 9CMT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MJ2 Structure of the dimerization domain of the human polyoma, JC virus agnoprotein is an amphipathic alpha-helix. Deposited 2013-12-23	Different construct Different mutation/modification 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 17–52（36 aa） Fragment：UNP residues 17-52	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3；293 K；Ionic strength (raw mmCIF value) no salts；Pressure ambient NMR measurement conditions pH 3；303 K；Ionic strength (raw mmCIF value) no salts；Pressure ambient NMR measurement conditions pH 3；313 K；Ionic strength (raw mmCIF value) no salts；Pressure ambient NMR sample composition 0.5 mM AGNO, 70 v/v H2O, 30 v/v [U-100% 2H] TFE, water with 30% (v/v) TFE (Trifluoroethanol, CF3CH2OH) \| water with 30% (v/v) TFE (Trifluoroethanol, CF3CH2OH)	Resolution not provided
5NHQ Nuclear Magnetic Resonance Structure of the Human Polyoma JC Virus Agnoprotein Deposited 2017-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–71（71 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3；313 K；Ionic strength (raw mmCIF value) 200 mM NaCl；Pressure pa NMR sample composition 0.2 mM no labelling agnoprotein, trifluoroethanol/water \| trifluoroethanol/water	Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

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
最后修订 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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.13 Å
Radius of gyration Rg (electron density) rg_electron	24.37 Å
Forward intensity I(0) i0	19003100.00
Molecular weight molecular_weight	33621.0 kDa
Excluded volume excluded_volume	42319 Å³
Envelope volume envelope_volume	54552 Å³
Hydration-shell volume shell_volume	19916 Å³
Envelope diameter envelope_diameter	86.5 Å
Shell Rg shell_rg	29.69 Å
Envelope Rg envelope_rg	24.63 Å
Shape Rg shape_rg	24.33 Å
Total Rg total_rg	25.21 Å
Total atoms total_atoms	2369
Residues n_residues	290
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	84.2 Å
Rg (real space) rg_real	25.21 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	1.9000e+07
I(0) uncertainty (real space) i0_real_error	2.5960e+05
Rg (reciprocal space) rg_reciprocal	25.18 Å
I(0) (reciprocal space) i0_reciprocal	19000000.0000
Solution quality estimate total_estimate	0.8792
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.371
Kurtosis Kurtosis kurtosis	-0.440
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3592000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.811; Smooth: 0.956

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

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 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/cm/9cmt/9cmt.fit
pddf	/app/data/pr_computation/cm/9cmt/9cmt.pr.out
profile	/app/data/saxs_computation/cm/9cmt/9cmt.dat

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

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)