4j2l

Crystal Structure of AXH domain complexed with Capicua

Method: X-RAY DIFFRACTION Dmax: 85.4 Å Quality: GOOD

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

Ataxin-1

Homo sapiens

UniProt P54253

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 562–688 Fragment:AXH domain, UNP residues 562-688 Protein capicua homolog × 1 (Q96RK0) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;293 K;1.6M NaCl, 3%(v/v) glycerol, 16%(w/v) PEG3350, 1mM L-Glutathione, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.15 Å R-free 0.294
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 562–688 Fragment:AXH domain, UNP residues 562-688 Protein capicua homolog × 1 (Q96RK0) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;293 K;1.6M NaCl, 3%(v/v) glycerol, 16%(w/v) PEG3350, 1mM L-Glutathione, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.15 Å R-free 0.294

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 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ATX1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–129; UniProt 562–688 Author chain B; PDBConstruct 3–129; UniProt 562–688

Protein capicua homolog

Homo sapiens

UniProt Q96RK0

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 21–48 Fragment:UNP residues 21-48 Ataxin-1 × 1 (P54253) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;293 K;1.6M NaCl, 3%(v/v) glycerol, 16%(w/v) PEG3350, 1mM L-Glutathione, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.15 Å R-free 0.294
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 21–48 Fragment:UNP residues 21-48 Ataxin-1 × 1 (P54253) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;293 K;1.6M NaCl, 3%(v/v) glycerol, 16%(w/v) PEG3350, 1mM L-Glutathione, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.15 Å R-free 0.294

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 CIC_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–28; UniProt 21–48 Author chain D; PDBConstruct 1–28; UniProt 21–48

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 4j2l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4j2l
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4j2l
Deposition date deposition_date2013-02-04
Structure title titleCrystal Structure of AXH domain complexed with Capicua
Keywords keywordsAXH domain, homodimerization protein-protein interaction, Capciua, ATXN1, TRANSCRIPTION REGULATOR; TRANSCRIPTION REGULATOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.49
Radius of gyration Rg (electron density) rg_electron24.64
Forward intensity I(0) i017151200.00
Molecular weight molecular_weight32655.0 kDa
Excluded volume excluded_volume41368 ų
Envelope volume envelope_volume50265 ų
Hydration-shell volume shell_volume18477 ų
Envelope diameter envelope_diameter86.3
Shell Rg shell_rg29.48
Envelope Rg envelope_rg24.74
Shape Rg shape_rg24.60
Total Rg total_rg25.41
Total atoms total_atoms2302
Residues n_residues294
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 dmax85.4
Rg (real space) rg_real25.73
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real1.7150e+07
I(0) uncertainty (real space) i0_real_error2.7260e+05
Rg (reciprocal space) rg_reciprocal25.66
I(0) (reciprocal space) i0_reciprocal17150000.0000
Solution quality estimate total_estimate0.8168
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.0
Skewness Skewness skewness0.521
Kurtosis Kurtosis kurtosis-0.480
Angular range angular_range— – 0.3100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3396000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.670; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.708; Smooth: 0.896

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4j2la_
Class classb — All beta proteins
Fold Fold foldb.145 — AXH domain
Superfamily Superfamily superfamilyb.145.1 — AXH domain
Family Family familyb.145.1.1 — AXH domain
Domain ID domain_idd4j2lb_
Class classb — All beta proteins
Fold Fold foldb.145 — AXH domain
Superfamily Superfamily superfamilyb.145.1 — AXH domain
Family Family familyb.145.1.1 — AXH domain

8. Citations (1)

9. Files and Curves (10)