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2k42

Solution Structure of the GTPase Binding Domain of WASP in Complex with EspFU, an EHEC Effector

Method: SOLUTION NMR Dmax: 39.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Wiskott-Aldrich syndrome protein

Homo sapiens

UniProt P42768

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 242–310 Fragment：CRIB domain, UNP residues 242-310 ESPFU × 1 （Q8X2D5） SOLUTION NMR NMR measurement conditions：pH 6.8；298.15 K；Pressure ambient NMR sample composition：1~1.5 mM [U-100% 13C; U-100% 15N] GBD/R33 complex, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1~1.5 mM [U-100% 13C; U-100% 15N] GBD/R33 complex, 100% D2O | 100% 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 2K42 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CEE SOLUTION STRUCTURE OF CDC42 IN COMPLEX WITH THE GTPASE BINDING DOMAIN OF WASP Deposited 1999-03-08 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 230–288（59 aa） Fragment：GTPASE BINDING DOMAIN OF WASP
Not recorded MG MAGNESIUM ION × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50mM；Pressure 1
Resolution not provided
1EJ5 SOLUTION STRUCTURE OF THE AUTOINHIBITED CONFORMATION OF WASP Deposited 2000-02-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 242–310（69 aa）
Chain A 461–492（32 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 75mM；Pressure ambient
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 75mM；Pressure ambient
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 75mM；Pressure ambient
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 75mM；Pressure ambient
NMR sample composition 1.6 mM protein U-15N; 25 mM phosphate buffer pH 6.5, 50 mM NaCl, 1 mM EDTA, 2 mM DTT | 90% H2O/10% D2O
NMR sample composition 1.6 mM protein U-15N,13C; 25 mM phosphate buffer pH 6.5, 50 mM NaCl, 1 mM EDTA, 2 mM DTT | 90% H2O/10% D2O
NMR sample composition 1.6 mM protein U-15N, 10% 13C; 25 mM phosphate buffer pH 6.5, 50 mM NaCl, 1 mM EDTA, 2 mM DTT | 90% H2O/10% D2O
NMR sample composition 1.6 mM protein U-15N,13C; 25 mM phosphate buffer pH 6.5, 50 mM NaCl, 1 mM EDTA, 2 mM DTT | 100% D2O
Resolution not provided
1T84 Solution structure of the Wiskott-Aldrich Syndrome Protein (WASP) autoinhibited core domain complexed with (S)-wiskostatin, a small molecule inhibitor Deposited 2004-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 242–310（69 aa） Fragment：core autoinhibited domain (GTPase binding domain is covalently linked to the cofilin homology and acidic regions)
Chain A 361–492（132 aa） Fragment：core autoinhibited domain (GTPase binding domain is covalently linked to the cofilin homology and acidic regions)
Not recorded WSK (2S)-1-(3,6-DIBROMO-9H-CARBAZOL-9-YL)-3-(DIMETHYLAMINO)PROPAN-2-OL × 1 SOLUTION NMR
NMR measurement conditions pH 5；298 K；Ionic strength (raw mmCIF value) 20mM；Pressure ambient
NMR sample composition 1mM WASP U-15N,13C; 1mM (S)-wiskostatin | 20 mM Acetate-d3 pH 5.0; 20mM NaCl; 1mM DTT-d10; 5% DMSO-d6; 90% H2O/10% D2O or 100% D2O
Resolution not provided
2OT0 Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with a C-terminal peptide of Wiskott-Aldrich syndrome protein Deposited 2007-02-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 488–502（15 aa）
Chain F 488–502（15 aa）
Chain G 488–502（15 aa）
Chain H 488–502（15 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；HEPES, MgCl2, PEG 550 MME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.05 Å R-free 0.200

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

View Construct and Data Evidence
UniProt name WASP_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–72； UniProt 242–310

ESPFU

Escherichia coli O157:H7

UniProt Q8X2D5

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 B； UniProt 268–300 Fragment：UNP residues 268-300 Wiskott-Aldrich syndrome protein × 1 （P42768） SOLUTION NMR NMR measurement conditions：pH 6.8；298.15 K；Pressure ambient NMR sample composition：1~1.5 mM [U-100% 13C; U-100% 15N] GBD/R33 complex, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1~1.5 mM [U-100% 13C; U-100% 15N] GBD/R33 complex, 100% D2O | 100% 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 2K42 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2KXC 1H, 13C, and 15N Chemical Shift Assignments for IRTKS-SH3 and EspFu-R47 complex Deposited 2010-04-30 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 268–314（47 aa） Fragment：EspFu-R47 domain, UNP residues 268-314
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure AMBIENT
NMR sample composition 0.48 mM [U-98% 13C; U-98% 15N] IRTKS-SH3-1, 0.48 mM EspFu-R47-2, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] EspFu-R47-3, 0.9 mM IRTKS-SH3-4, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8X2D5_ECO57
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 4–36； UniProt 268–300

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 2k42

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2k42
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2k42
Deposition date deposition_date2008-05-27
Structure title titleSolution Structure of the GTPase Binding Domain of WASP in Complex with EspFU, an EHEC Effector
Keywords keywordsWASP, EspFU, GBD, autoinhibition, Cytoplasm, Cytoskeleton, Disease mutation, Phosphoprotein, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.90 Å
Radius of gyration Rg (electron density) rg_electron14.49 Å
Forward intensity I(0) i0953091000.00
Molecular weight molecular_weight243550.0 kDa
Excluded volume excluded_volume297630 ų
Envelope volume envelope_volume51823 ų
Hydration-shell volume shell_volume20769 ų
Envelope diameter envelope_diameter71.4 Å
Shell Rg shell_rg28.00 Å
Envelope Rg envelope_rg22.26 Å
Shape Rg shape_rg14.47 Å
Total Rg total_rg14.89 Å
Total atoms total_atoms33520
Residues n_residues2160
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 dmax39.5 Å
Rg (real space) rg_real13.90 Å
Rg uncertainty (real space) rg_real_error0.05 Å
I(0) (real space) i0_real9.0560e+08
I(0) uncertainty (real space) i0_real_error7.3920e+06
Rg (reciprocal space) rg_reciprocal15.00 Å
I(0) (reciprocal space) i0_reciprocal953100000.0000
Solution quality estimate total_estimate0.6775
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.5 Å
Skewness Skewness skewness0.206
Kurtosis Kurtosis kurtosis-0.230
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha2.7390
Highest regularization parameter α highest_alpha357800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.007; Oscil: 0.960; Stabil: 0.985; Sysdev: 0.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2k42A00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology810 — SerineThreonine-protein kinase PAK-alpha; Chain A
Homologous superfamily homologous superfamily10 — CRIB domain
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8. Citations (1)

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9. Files and Curves (10)