← Back to search
4quc

Crystal structure of chromodomain of Rhino

Method: X-RAY DIFFRACTION Dmax: 42.5 Å Quality: GOOD
▼

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

RE36324p

Drosophila melanogaster

UniProt Q7JXA8

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 19–85 Fragment：chromodomain No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2M Sodium nitrate and 20%(w/v) PEG3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.50 Å R-free 0.253

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 4QUC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4QUF crystal structure of chromodomain of Rhino with H3K9me3 Deposited 2014-07-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–85（67 aa）
Chain B 19–85（67 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2 M ammonium nitrate and 20% PEG3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.249
4QUF crystal structure of chromodomain of Rhino with H3K9me3 Deposited 2014-07-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 19–85（67 aa）
Chain D 19–85（67 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2 M ammonium nitrate and 20% PEG3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.249
4QUF crystal structure of chromodomain of Rhino with H3K9me3 Deposited 2014-07-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 19–85（67 aa）
Chain F 19–85（67 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2 M ammonium nitrate and 20% PEG3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.249
4U68 Crystal structure of Rhino chromodomain in complex with H3K9me3 Deposited 2014-07-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 20–90（71 aa） Fragment：chromodomain, UNP residues 20-90
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；290 K；30 %(v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, 25 % (w/v) PEG 1500
Resolution 1.80 Å R-free 0.206
4U68 Crystal structure of Rhino chromodomain in complex with H3K9me3 Deposited 2014-07-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 20–90（71 aa） Fragment：chromodomain, UNP residues 20-90
Chain C 20–90（71 aa） Fragment：chromodomain, UNP residues 20-90
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；290 K；30 %(v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, 25 % (w/v) PEG 1500
Resolution 1.80 Å R-free 0.206

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q7JXA8_DROME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–68； UniProt 19–85

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 4quc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4quc
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id4quc
Deposition date deposition_date2014-07-10
Structure title titleCrystal structure of chromodomain of Rhino
Keywords keywordshistone binding, protein binding; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier12.74 Å
Radius of gyration Rg (electron density) rg_electron11.37 Å
Forward intensity I(0) i0964458.00
Molecular weight molecular_weight6525.0 kDa
Excluded volume excluded_volume8227 ų
Envelope volume envelope_volume9297 ų
Hydration-shell volume shell_volume7491 ų
Envelope diameter envelope_diameter39.2 Å
Shell Rg shell_rg16.26 Å
Envelope Rg envelope_rg11.75 Å
Shape Rg shape_rg11.38 Å
Total Rg total_rg12.75 Å
Total atoms total_atoms461
Residues n_residues56
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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 dmax42.5 Å
Rg (real space) rg_real12.68 Å
Rg uncertainty (real space) rg_real_error0.30 Å
I(0) (real space) i0_real9.6450e+05
I(0) uncertainty (real space) i0_real_error1.0790e+04
Rg (reciprocal space) rg_reciprocal12.69 Å
I(0) (reciprocal space) i0_reciprocal964500.0000
Solution quality estimate total_estimate0.8891
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.6 Å
Skewness Skewness skewness0.120
Kurtosis Kurtosis kurtosis-0.425
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha111100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.972
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4quca_
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.13 — Chromo domain-like
Family Family familyb.34.13.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id4qucA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40 —
▶

8. Citations (1)

▶

9. Files and Curves (10)