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- PDB-2ifs: Structure of the N-WASP EVH1 domain in complex with an extended W... -

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Basic information

Entry
Database: PDB / ID: 2ifs
TitleStructure of the N-WASP EVH1 domain in complex with an extended WIP peptide
ComponentsWiskott-Aldrich Syndrome Protein interacting protein and Neural Wiskott-Aldrich syndrome protein chimera
KeywordsSIGNALING PROTEIN / Wiskott-Aldrich syndrome / verprolin / Polyproline / protein-protein complex
Function / homology
Function and homology information


negative regulation of membrane tubulation / spindle localization / membrane invagination / positive regulation of clathrin-dependent endocytosis / postsynaptic actin cytoskeleton organization / plasma membrane tubulation / postsynapse organization / negative regulation of lymphocyte migration / vesicle transport along actin filament / regulation of cell projection assembly ...negative regulation of membrane tubulation / spindle localization / membrane invagination / positive regulation of clathrin-dependent endocytosis / postsynaptic actin cytoskeleton organization / plasma membrane tubulation / postsynapse organization / negative regulation of lymphocyte migration / vesicle transport along actin filament / regulation of cell projection assembly / actin cap / profilin binding / actin filament-based movement / vesicle organization / cytoskeletal anchor activity / vesicle budding from membrane / positive regulation of chemotaxis / response to other organism / dendritic spine morphogenesis / actin polymerization or depolymerization / protein-containing complex localization / regulation of postsynapse organization / positive regulation of filopodium assembly / cell leading edge / CDC42 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / cytoskeletal protein binding / ruffle / actin filament polymerization / RAC1 GTPase cycle / protein folding chaperone / actin filament / FCGR3A-mediated phagocytosis / response to bacterium / SH3 domain binding / Regulation of actin dynamics for phagocytic cup formation / lamellipodium / actin cytoskeleton / regulation of protein localization / actin binding / actin cytoskeleton organization / protein-containing complex assembly / cytoplasmic vesicle / postsynapse / Golgi membrane / cell division / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / 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 ...: / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Actin nucleation-promoting factor WASL / WAS/WASL-interacting protein family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodSOLUTION NMR / AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
AuthorsVolkman, B.F. / Peterson, F.C. / Deng, Q.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Multiple WASP-interacting protein recognition motifs are required for a functional interaction with N-WASP.
Authors: Peterson, F.C. / Deng, Q. / Zettl, M. / Prehoda, K.E. / Lim, W.A. / Way, M. / Volkman, B.F.
History
DepositionSep 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 14, 2012Group: Other
Revision 1.4Sep 2, 2020Group: Data collection / Database references / Structure summary
Category: entity / pdbx_nmr_software / struct_ref_seq_dif
Item: _entity.pdbx_description / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.5May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999sequence Fusion protein consisting of Wiskott-Aldrich Syndrome Protien interacting protein (WIP), ...sequence Fusion protein consisting of Wiskott-Aldrich Syndrome Protien interacting protein (WIP), GGLVPRGSGG Linker, and neural Wiskott-Aldrich Syndrom Protein (N-WASP)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Wiskott-Aldrich Syndrome Protein interacting protein and Neural Wiskott-Aldrich syndrome protein chimera


Theoretical massNumber of molelcules
Total (without water)19,3271
Polymers19,3271
Non-polymers00
Water00
1


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

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Components

#1: Protein Wiskott-Aldrich Syndrome Protein interacting protein and Neural Wiskott-Aldrich syndrome protein chimera / N-WASP


Mass: 19326.990 Da / Num. of mol.: 1
Fragment: WIP peptide (residues 451-485) and N-WASP EVH1 domain (Residues 26-147)
Source method: isolated from a genetically manipulated source
Details: fusion protein / Source: (gene. exp.) Homo sapiens, Rattus norvegicus / Genus: Homo, Rattus / Species: , / Strain: , / Gene: WASPIP, wasl / Plasmid: pBH4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43516, UniProt: O08816

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY (AROMATIC)

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Sample preparation

DetailsContents: 1.0 mM U-15N/13C protein, 20 mM sodium phosphate, 1 mM Dithiothreitol, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.044 mM / pH: 7 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M.refinement
XwinNMR3.5Brukercollection
NMRPipe2004Delagio,F. et al.processing
XEASY1.3Eccles, C., Guntert, P., Billeter, M., Wuthrich, K.data analysis
SPSCAN1.1.0R.W. Glaserdata analysis
GARANT2.1C. Bartelsdata analysis
CYANA2.1Guntert, P.structural calculation
RefinementMethod: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT, ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 2411 NOE CONSTRAINTS ( 383 INTRA, 473 SEQUENTIAL, 386 MEDIUM and 922 INTRAMOLECULAR LONG RANGE - EVH1 DOMAIN, 247 INTERMOLECULAR WIP-EVH1 CONSTRAINTS) AND ...Details: STRUCTURES ARE BASED ON A TOTAL OF 2411 NOE CONSTRAINTS ( 383 INTRA, 473 SEQUENTIAL, 386 MEDIUM and 922 INTRAMOLECULAR LONG RANGE - EVH1 DOMAIN, 247 INTERMOLECULAR WIP-EVH1 CONSTRAINTS) AND 253 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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