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- PDB-1mke: Structure of the N-WASP EVH1 Domain-WIP complex -

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Basic information

Entry
Database: PDB / ID: 1mke
TitleStructure of the N-WASP EVH1 Domain-WIP complex
ComponentsFusion protein consisting of Wiskott-Aldrich syndrome protein interacting protein (WIP), GSGSG linker, and Neural Wiskott-Aldrich syndrome protein (N-WASP)
KeywordsPROTEIN BINDING / 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 / plasma membrane tubulation / negative regulation of lymphocyte migration / postsynapse organization / regulation of cell projection assembly / actin cap / actin filament-based movement ...negative regulation of membrane tubulation / spindle localization / membrane invagination / positive regulation of clathrin-dependent endocytosis / plasma membrane tubulation / negative regulation of lymphocyte migration / postsynapse organization / regulation of cell projection assembly / actin cap / actin filament-based movement / vesicle organization / postsynaptic actin cytoskeleton organization / profilin binding / vesicle budding from membrane / positive regulation of chemotaxis / response to other organism / actin polymerization or depolymerization / vesicle transport along actin filament / protein-containing complex localization / dendritic spine morphogenesis / regulation of postsynapse organization / positive regulation of filopodium assembly / cell leading edge / CDC42 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / protein folding chaperone / ruffle / RAC1 GTPase cycle / cytoskeletal protein binding / actin filament polymerization / actin filament / FCGR3A-mediated phagocytosis / response to bacterium / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / regulation of protein localization / actin cytoskeleton / lamellipodium / actin binding / cytoplasmic vesicle / actin cytoskeleton organization / postsynapse / protein-containing complex assembly / cell division / Golgi membrane / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / 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 / WH2 domain profile. ...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 speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsVolkman, B.F. / Prehoda, K.E. / Scott, J.A. / Peterson, F.C. / Lim, W.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Structure of the N-WASP EVH1 Domain-WIP Complex. Insight into the Molecular Basis of Wiskott-Aldrich Syndrome.
Authors: Volkman, B.F. / Prehoda, K.E. / Scott, J.A. / Peterson, F.C. / Lim, W.A.
History
DepositionAug 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Fusion protein consisting of Wiskott-Aldrich syndrome protein interacting protein (WIP), GSGSG linker, and Neural Wiskott-Aldrich syndrome protein (N-WASP)


Theoretical massNumber of molelcules
Total (without water)17,4231
Polymers17,4231
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)21 / 50LOWEST TARGET FUNCTION
RepresentativeModel #1minimized average structure

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Components

#1: Protein Fusion protein consisting of Wiskott-Aldrich syndrome protein interacting protein (WIP), GSGSG linker, and Neural Wiskott-Aldrich syndrome protein (N-WASP) / / WIP - N-WASP


Mass: 17422.832 Da / Num. of mol.: 1 / Fragment: WIP peptide and N-WASP EVH1 domain
Source method: isolated from a genetically manipulated source
Details: FUSION PROTEIN COMPRISES RESIDUES 461-485 of WIP, a GSGSG linker sequence, and residues 26-147 (EVH1 domain) of N-WASP
Source: (gene. exp.) Rattus norvegicus, Homo sapiens / Genus: Rattus, Homo / Species: , / Strain: , / 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
1223D 13C-separated NOESY
NMR detailsText: REPRESENTATIVE CONFORMER (MODEL 1) IS MINIMIZED AVERAGE STRUCTURE.

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N protein 20 mM PO4 buffer 1 mM dithiothreitol90% H2O/10% D2O
2U-13C/15N protein 20 mM PO4 buffer 1 mM dithiothreitol90% H2O/10% D2O
Sample conditionsIonic strength: 20 mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentert, P.structure solution
XwinNMR3Brukercollection
XEASY1.3Guentert, P.data analysis
NMRPipeDelaglio, F.processing
DYANA1.5Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: final structures were derived from a total of 1884 non-trivial NOE distance constraints, including 135 restraints between residues of the WIP peptide and the EVH1 domain. 143 phi and psi ...Details: final structures were derived from a total of 1884 non-trivial NOE distance constraints, including 135 restraints between residues of the WIP peptide and the EVH1 domain. 143 phi and psi torsion angle constraints were generated from chemical shift database searching using the program TALOS
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: LOWEST TARGET FUNCTION / Conformers calculated total number: 50 / Conformers submitted total number: 21

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