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- PDB-1t84: Solution structure of the Wiskott-Aldrich Syndrome Protein (WASP)... -

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Basic information

Entry
Database: PDB / ID: 1t84
TitleSolution structure of the Wiskott-Aldrich Syndrome Protein (WASP) autoinhibited core domain complexed with (S)-wiskostatin, a small molecule inhibitor
ComponentsWiskott-Aldrich syndrome protein
KeywordsSIGNALING PROTEIN / ALPHA HELIX / BETA-HAIRPIN TURN
Function / homology
Function and homology information


regulation of T cell antigen processing and presentation / regulation of actin polymerization or depolymerization / Cdc42 protein signal transduction / GTPase regulator activity / actin filament-based movement / negative regulation of cell motility / vesicle membrane / actin polymerization or depolymerization / regulation of stress fiber assembly / regulation of lamellipodium assembly ...regulation of T cell antigen processing and presentation / regulation of actin polymerization or depolymerization / Cdc42 protein signal transduction / GTPase regulator activity / actin filament-based movement / negative regulation of cell motility / vesicle membrane / actin polymerization or depolymerization / regulation of stress fiber assembly / regulation of lamellipodium assembly / negative regulation of stress fiber assembly / endosomal transport / positive regulation of double-strand break repair via homologous recombination / RHOJ GTPase cycle / phospholipase binding / CDC42 GTPase cycle / Generation of second messenger molecules / RHO GTPases Activate WASPs and WAVEs / epidermis development / phagocytic vesicle / RAC1 GTPase cycle / actin filament polymerization / T cell activation / actin filament / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / defense response / small GTPase binding / SH3 domain binding / cellular response to type II interferon / cell-cell junction / blood coagulation / actin cytoskeleton / site of double-strand break / actin binding / protein-containing complex assembly / immune response / protein kinase binding / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
SerineThreonine-protein kinase PAK-alpha; Chain A / CRIB domain / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 ...SerineThreonine-protein kinase PAK-alpha; Chain A / CRIB domain / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain / WH2 domain profile. / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / PH-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-WSK / Actin nucleation-promoting factor WAS
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing; torsion angle dynamics
AuthorsPeterson, J.R. / Bickford, L.C. / Morgan, D. / Kim, A.S. / Ouerfelli, O. / Kirschner, M.W. / Rosen, M.K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Chemical inhibition of N-WASP by stabilization of a native autoinhibited conformation.
Authors: Peterson, J.R. / Bickford, L.C. / Morgan, D. / Kim, A.S. / Ouerfelli, O. / Kirschner, M.W. / Rosen, M.K.
History
DepositionMay 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999Sequence The polyproline region present in the original gene sequence (residues 311-460) has been ...Sequence The polyproline region present in the original gene sequence (residues 311-460) has been replaced by a hexapeptide linker with the sequence Gly-Gly-Ser-Gly-Gly-Ser.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Wiskott-Aldrich syndrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0302
Polymers11,6041
Non-polymers4261
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Wiskott-Aldrich syndrome protein / WASp


Mass: 11603.597 Da / Num. of mol.: 1
Fragment: core autoinhibited domain (GTPase binding domain is covalently linked to the cofilin homology and acidic regions)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WASP (residues 242-310 and 461-492) / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42768
#2: Chemical ChemComp-WSK / (2S)-1-(3,6-DIBROMO-9H-CARBAZOL-9-YL)-3-(DIMETHYLAMINO)PROPAN-2-OL / (S)-WISKOSTATIN


Mass: 426.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18Br2N2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HCC-TOCSY
121CCC-TOCSY
131(H)CCH-TOCSY
1413D-13C-separated NOESY aliphatic
1513D-13C-separated NOESY aromatic
1613D 15N-separated NOESY
1714D 13C-separated NOESY
1814D 13C/15N-separated NOESY
1913D 13C-edited 12C-filtered NOESY

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Sample preparation

DetailsContents: 1mM WASP U-15N,13C; 1mM (S)-wiskostatin
Solvent system: 20 mM Acetate-d3 pH 5.0; 20mM NaCl; 1mM DTT-d10; 5% DMSO-d6; 90% H2O/10% D2O or 100% D2O
Sample conditionsIonic strength: 20mM / pH: 5.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.7Baxprocessing
NMRView2.1.2Johnsondata analysis
VNMR6.1Bdata analysis
X-PLOR3.851Brungerstructure solution
ARIA1Nilgesstructure solution
ARIA1Nilgesrefinement
RefinementMethod: simulated annealing; torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 1466 restraints. 1298 are NOE-derived intramolecular distance restraints; 30 are NOE-derived intermolecular distance restraints; 138 are dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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