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1t84

Solution structure of the Wiskott-Aldrich Syndrome Protein (WASP) autoinhibited core domain complexed with (S)-wiskostatin, a small molecule inhibitor

Method: SOLUTION NMR Dmax: 45.4 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 242–310 Chain A； UniProt 361–492 Fragment：core autoinhibited domain (GTPase binding domain is covalently linked to the cofilin homology and acidic regions) 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

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 1T84 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 mutation/modification Different oligomeric state 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 ligand/ion 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
2K42 Solution Structure of the GTPase Binding Domain of WASP in Complex with EspFU, an EHEC Effector Deposited 2008-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 242–310（69 aa） Fragment：CRIB domain, UNP residues 242-310
Not recorded No recorded non-water small molecule 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
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 ligand/ion 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 1–69； UniProt 242–310 Author chain A； PDBConstruct 76–107； UniProt 361–492

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 1t84

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1t84
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1t84
Deposition date deposition_date2004-05-11
Structure title titleSolution structure of the Wiskott-Aldrich Syndrome Protein (WASP) autoinhibited core domain complexed with (S)-wiskostatin, a small molecule inhibitor
Keywords keywordsALPHA HELIX, BETA-HAIRPIN TURN, 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_guinier16.82 Å
Radius of gyration Rg (electron density) rg_electron15.98 Å
Forward intensity I(0) i01006350000.00
Molecular weight molecular_weight240170.0 kDa
Excluded volume excluded_volume288660 ų
Envelope volume envelope_volume58850 ų
Hydration-shell volume shell_volume22167 ų
Envelope diameter envelope_diameter76.8 Å
Shell Rg shell_rg29.51 Å
Envelope Rg envelope_rg23.58 Å
Shape Rg shape_rg16.01 Å
Total Rg total_rg16.21 Å
Total atoms total_atoms32440
Residues n_residues2140
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 dmax45.4 Å
Rg (real space) rg_real15.85 Å
Rg uncertainty (real space) rg_real_error0.08 Å
I(0) (real space) i0_real9.5820e+08
I(0) uncertainty (real space) i0_real_error8.0380e+06
Rg (reciprocal space) rg_reciprocal16.94 Å
I(0) (reciprocal space) i0_reciprocal1006000000.0000
Solution quality estimate total_estimate0.6764
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary17.7 Å
Skewness Skewness skewness0.345
Kurtosis Kurtosis kurtosis-0.359
Angular range angular_range— – 0.4750 Å−1
Current regularization parameter α current_alpha4.1300
Highest regularization parameter α highest_alpha596000.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.002; Oscil: 0.952; Stabil: 0.979; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; 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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1t84a_
Class classa — All alpha proteins
Fold Fold folda.68 — Wiscott-Aldrich syndrome protein, WASP, C-terminal domain
Superfamily Superfamily superfamilya.68.1 — Wiscott-Aldrich syndrome protein, WASP, C-terminal domain
Family Family familya.68.1.1 — Wiscott-Aldrich syndrome protein, WASP, C-terminal domain

CATH v4.4 (1 domains)

Domain ID domain_id1t84A00
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)