9cdw

Crystal structure of HP1alpha chromoshadow domain in complex with KAP1 peptide

Method: X-RAY DIFFRACTION Dmax: 82.6 Å Quality: GOOD

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

Chromobox protein homolog 5

Homo sapiens

UniProt P45973

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 A; UniProt 111–174 Chain C; UniProt 111–174 Not recorded Transcription intermediary factor 1-beta peptide × 1 (Q13263) 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 111–174 Chain D; UniProt 111–174 Not recorded Transcription intermediary factor 1-beta peptide × 1 (Q13263) 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

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.

5 other PDB entries and 9 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 1–64; UniProt 111–174 Author chain B; PDBConstruct 1–64; UniProt 111–174 Author chain C; PDBConstruct 1–64; UniProt 111–174 Author chain D; PDBConstruct 1–64; UniProt 111–174

Transcription intermediary factor 1-beta peptide

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 485–490 Not recorded Chromobox protein homolog 5 × 2 (P45973) 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 485–490 Not recorded Chromobox protein homolog 5 × 2 (P45973) 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

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 9 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 E; PDBConstruct 1–6; UniProt 485–490 Author chain F; PDBConstruct 1–6; UniProt 485–490

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 9cdw

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9cdw
Deposition date deposition_date2024-06-25
最后修订 last_revision2025-06-11
Structure title titleCrystal structure of HP1alpha chromoshadow domain in complex with KAP1 peptide
Keywords keywordsHP1, CSD domain, KAP1, TRANSCRIPTION, TRANSCRIPTION-PEPTIDE complex; TRANSCRIPTION/PEPTIDE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier22.45
Radius of gyration Rg (electron density) rg_electron22.09
Forward intensity I(0) i016433900.00
Molecular weight molecular_weight30907.0 kDa
Excluded volume excluded_volume38901 ų
Envelope volume envelope_volume49930 ų
Hydration-shell volume shell_volume19947 ų
Envelope diameter envelope_diameter88.0
Shell Rg shell_rg27.55
Envelope Rg envelope_rg22.52
Shape Rg shape_rg22.15
Total Rg total_rg22.71
Total atoms total_atoms2166
Residues n_residues268
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 dmax82.6
Rg (real space) rg_real22.51
Rg uncertainty (real space) rg_real_error0.84
I(0) (real space) i0_real1.6430e+07
I(0) uncertainty (real space) i0_real_error2.7610e+05
Rg (reciprocal space) rg_reciprocal22.49
I(0) (reciprocal space) i0_reciprocal16430000.0000
Solution quality estimate total_estimate0.7536
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.8
Skewness Skewness skewness0.470
Kurtosis Kurtosis kurtosis-0.027
Angular range angular_range— – 0.3550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4201000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.636; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.886; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)