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1wxa

Solution Structure of Ras-binding Domain in Mouse AF-6 Protein

Method: SOLUTION NMR Dmax: 58.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Afadin

Mus musculus

UniProt Q9QZQ1

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 246–348 Fragment：Ras-binding domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 100mM；Pressure ambient NMR sample composition：1.28mM protein U-15N, 13C; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O | 90% H2O/10% D2O Resolution not provided

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 1WXA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1WLN Solution structure of the FHA domain of mouse Afadin 6 Deposited 2004-06-28 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 381–487（107 aa） Fragment：FHA domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 0.7mM FHA domain; U-15N,13C; 20mM phosphate buffer NA; 100mM NaCl; 0.02% NaN3; 1mMDTT | 90% H2O/10% D2O
Resolution not provided
3AXA Crystal structure of afadin PDZ domain in complex with the C-terminal peptide from nectin-3 Deposited 2011-03-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1003–1095（93 aa） Fragment：PDZ domain (UNP 1003-1095), C-terminal peptide (UNP 544-549)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.78 Å R-free 0.263
3AXA Crystal structure of afadin PDZ domain in complex with the C-terminal peptide from nectin-3 Deposited 2011-03-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1003–1095（93 aa） Fragment：PDZ domain (UNP 1003-1095), C-terminal peptide (UNP 544-549)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.78 Å R-free 0.263
6AMB Crystal Structure of the Afadin RA1 domain in complex with HRAS Deposited 2017-08-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 38–136（99 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.9；297 K；PEG3350, K2HPO4
Resolution 2.50 Å R-free 0.266
9DVA F-actin binding interface of alpha-E-catenin ABD (cadherin-catenin complex) and afadin Deposited 2024-10-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1393–1602（210 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

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

View Construct and Data Evidence
UniProt name AFAD_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–110； UniProt 246–348

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 1wxa

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1wxa
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1wxa
Deposition date deposition_date2005-01-20
Structure title titleSolution Structure of Ras-binding Domain in Mouse AF-6 Protein
Keywords keywords;Ras-binding domain, ubiquitin-like fold, AF-6 protein, Structural genomics, Afadin, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, CELL ADHESION ;; CELL ADHESION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.20 Å
Radius of gyration Rg (electron density) rg_electron14.41 Å
Forward intensity I(0) i0902630000.00
Molecular weight molecular_weight251560.0 kDa
Excluded volume excluded_volume313750 ų
Envelope volume envelope_volume38761 ų
Hydration-shell volume shell_volume17939 ų
Envelope diameter envelope_diameter63.5 Å
Shell Rg shell_rg24.43 Å
Envelope Rg envelope_rg18.76 Å
Shape Rg shape_rg14.39 Å
Total Rg total_rg14.67 Å
Total atoms total_atoms35200
Residues n_residues2320
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax58.8 Å
Rg (real space) rg_real15.16 Å
Rg uncertainty (real space) rg_real_error0.58 Å
I(0) (real space) i0_real9.0260e+08
I(0) uncertainty (real space) i0_real_error1.1700e+07
Rg (reciprocal space) rg_reciprocal15.16 Å
I(0) (reciprocal space) i0_reciprocal902600000.0000
Solution quality estimate total_estimate0.7995
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.9 Å
Skewness Skewness skewness0.290
Kurtosis Kurtosis kurtosis-0.105
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha431100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.517; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.838; Smooth: 0.999
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1wxaa1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.5 — Ras-binding domain, RBD
Domain ID domain_idd1wxaa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1wxaa3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id1wxaA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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8. Citations (1)

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9. Files and Curves (10)