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- PDB-2k42: Solution Structure of the GTPase Binding Domain of WASP in Comple... -

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Basic information

Entry
Database: PDB / ID: 2k42
TitleSolution Structure of the GTPase Binding Domain of WASP in Complex with EspFU, an EHEC Effector
Components
  • ESPFU
  • Wiskott-Aldrich syndrome protein
KeywordsSIGNALING PROTEIN / WASP / EspFU / GBD / autoinhibition / Cytoplasm / Cytoskeleton / Disease mutation / Phosphoprotein
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 / host cell cytoplasm / immune response / protein kinase binding / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Type III secretion protein EspF / TccP2/EspF(U)-like superfamily / EspF protein repeat / 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 ...Type III secretion protein EspF / TccP2/EspF(U)-like superfamily / EspF protein repeat / 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
Secreted effector protein EspF(U) / Actin nucleation-promoting factor WAS / Secreted effector protein EspF(U)
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli O157:H7 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsCheng, H.-C. / Skehan, B.M. / Campellone, K.G. / Leong, J.M. / Rosen, M.K.
CitationJournal: Nature / Year: 2008
Title: Structural mechanism of WASP activation by the enterohaemorrhagic E. coli effector EspF(U).
Authors: Cheng, H.C. / Skehan, B.M. / Campellone, K.G. / Leong, J.M. / Rosen, M.K.
History
DepositionMay 27, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Wiskott-Aldrich syndrome protein
B: ESPFU


Theoretical massNumber of molelcules
Total (without water)12,2002
Polymers12,2002
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 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Wiskott-Aldrich syndrome protein / WASp


Mass: 8128.908 Da / Num. of mol.: 1 / Fragment: CRIB domain, UNP residues 242-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WAS, IMD2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P42768
#2: Protein/peptide ESPFU / Tir-cytoskeleton coupling protein


Mass: 4070.681 Da / Num. of mol.: 1 / Fragment: UNP residues 268-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: tccP, ECs2715 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8X2D5, UniProt: P0DJ89*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D CBCA(CO)NH
1323D (H)CCH-TOCSY
1412D 1H-15N HSQC
1513D 1H-15N NOESY
1613D HNCO
1724D 13C-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11~1.5 mM [U-100% 13C; U-100% 15N] GBD/R33 complex, 90% H2O/10% D2O90% H2O/10% D2O
21~1.5 mM [U-100% 13C; U-100% 15N] GBD/R33 complex, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMGBD/R33 complex[U-100% 13C; U-100% 15N]1
1 mMGBD/R33 complex[U-100% 13C; U-100% 15N]2
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298.15 K

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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
ARIA2.1Linge, O'Donoghue and Nilgesstructure solution
ARIA2.1Linge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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