9osc

Crystal structure of HP1gamma chromoshadow domain in complex with KAP1 peptide

Method: X-RAY DIFFRACTION Dmax: 50.5 Å Quality: GOOD

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

Chromobox protein homolog 3

Homo sapiens

UniProt Q13185

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 110–176 Not recorded Transcription intermediary factor 1-beta × 1 (Q13263) 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

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.

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 1
Chains and sequence ranges Author chain A; PDBConstruct 1–67; UniProt 110–176

Transcription intermediary factor 1-beta

Homo sapiens

UniProt Q13263

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 C; UniProt 483–493 Not recorded Chromobox protein homolog 3 × 1 (Q13185) 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

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.

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

View Construct and Data Evidence
UniProt name TIF1B_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–11; UniProt 483–493

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9osc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9osc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9osc
Deposition date deposition_date2025-05-23
最后修订 last_revision2026-02-04
Structure title titleCrystal structure of HP1gamma chromoshadow domain in complex with KAP1 peptide
Keywords keywordsHP1, CSD domain, KAP1, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier13.84
Radius of gyration Rg (electron density) rg_electron12.64
Forward intensity I(0) i01371300.00
Molecular weight molecular_weight7863.0 kDa
Excluded volume excluded_volume9887 ų
Envelope volume envelope_volume11629 ų
Hydration-shell volume shell_volume8465 ų
Envelope diameter envelope_diameter50.8
Shell Rg shell_rg17.33
Envelope Rg envelope_rg13.18
Shape Rg shape_rg12.66
Total Rg total_rg13.83
Total atoms total_atoms552
Residues n_residues70
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax50.5
Rg (real space) rg_real13.86
Rg uncertainty (real space) rg_real_error0.35
I(0) (real space) i0_real1.3710e+06
I(0) uncertainty (real space) i0_real_error1.5730e+04
Rg (reciprocal space) rg_reciprocal13.85
I(0) (reciprocal space) i0_reciprocal1371000.0000
Solution quality estimate total_estimate0.8318
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.3
Skewness Skewness skewness0.393
Kurtosis Kurtosis kurtosis0.052
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha218000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.660; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.884; Smooth: 0.946

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)