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- PDB-1ej5: SOLUTION STRUCTURE OF THE AUTOINHIBITED CONFORMATION OF WASP -

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Basic information

Entry
Database: PDB / ID: 1ej5
TitleSOLUTION STRUCTURE OF THE AUTOINHIBITED CONFORMATION OF WASP
ComponentsWISKOTT-ALDRICH SYNDROME PROTEIN
KeywordsBLOOD CLOTTING / 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 / defense response / Regulation of actin dynamics for phagocytic cup formation / 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 / WH2 motif / Wiskott Aldrich syndrome homology region 2 / WH2 domain / WH2 domain profile. / WH1/EVH1 domain / WH1 domain ...SerineThreonine-protein kinase PAK-alpha; Chain A / CRIB domain / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / WH2 motif / Wiskott Aldrich syndrome homology region 2 / WH2 domain / WH2 domain profile. / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / 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
Actin nucleation-promoting factor WAS
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsKim, A.S. / Kakalis, L.T. / Abdul-Manan, N. / Liu, G.A. / Rosen, M.K.
CitationJournal: Nature / Year: 2000
Title: Autoinhibition and activation mechanisms of the Wiskott-Aldrich syndrome protein.
Authors: Kim, A.S. / Kakalis, L.T. / Abdul-Manan, N. / Liu, G.A. / Rosen, M.K.
History
DepositionFeb 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WISKOTT-ALDRICH SYNDROME PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,6041
Polymers11,6041
Non-polymers00
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 least restraint violations
RepresentativeModel #14lowest energy

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Components

#1: Protein WISKOTT-ALDRICH SYNDROME PROTEIN / WASP


Mass: 11603.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P42768

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2123D 13C-separated NOESY
2223D 15N-separated NOESY
2324D 13C-separated NOESY
2424D 13C/15N-separated NOESY
151HNHA
262(H)CCH-TOCSY
NMR detailsText: The structure was determined using standard 3D and 4D heteronuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.6 mM protein U-15N; 25 mM phosphate buffer pH 6.5, 50 mM NaCl, 1 mM EDTA, 2 mM DTT90% H2O/10% D2O
21.6 mM protein U-15N,13C; 25 mM phosphate buffer pH 6.5, 50 mM NaCl, 1 mM EDTA, 2 mM DTT90% H2O/10% D2O
31.6 mM protein U-15N, 10% 13C; 25 mM phosphate buffer pH 6.5, 50 mM NaCl, 1 mM EDTA, 2 mM DTT90% H2O/10% D2O
41.6 mM protein U-15N,13C; 25 mM phosphate buffer pH 6.5, 50 mM NaCl, 1 mM EDTA, 2 mM DTT100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
175mM 6.5 ambient 298 K
275mM 6.5 ambient 298 K
375mM 6.5 ambient 298 K
475mM 6.5 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
CNS0.3Brunger, Nilgesrefinement
XPLOR3.851Brungerrefinement
NMRPipe1.7Delaglioprocessing
NMRView2.1.2Jonhson, Blevinsdata analysis
VNMR6.1bVARIANcollection
ARIA1Nilgesrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 2713 restraints, 2494 are NOE-derived distance constraints, 182 dihedral angle restraints, 31 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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