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- PDB-1k1z: Solution structure of N-terminal SH3 domain mutant(P33G) of murine Vav -

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Basic information

Entry
Database: PDB / ID: 1k1z
TitleSolution structure of N-terminal SH3 domain mutant(P33G) of murine Vav
Componentsvav
KeywordsSIGNALING PROTEIN / SH3 / Proto-oncogene
Function / homology
Function and homology information


Azathioprine ADME / RAC2 GTPase cycle / CD28 dependent Vav1 pathway / Erythropoietin activates RAS / GPVI-mediated activation cascade / RHOA GTPase cycle / RHOG GTPase cycle / NRAGE signals death through JNK / RAC1 GTPase cycle / Signaling by SCF-KIT ...Azathioprine ADME / RAC2 GTPase cycle / CD28 dependent Vav1 pathway / Erythropoietin activates RAS / GPVI-mediated activation cascade / RHOA GTPase cycle / RHOG GTPase cycle / NRAGE signals death through JNK / RAC1 GTPase cycle / Signaling by SCF-KIT / VEGFR2 mediated vascular permeability / phosphorylation-dependent protein binding / G alpha (12/13) signalling events / PIP3 activates AKT signaling / Regulation of signaling by CBL / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / FCERI mediated MAPK activation / positive regulation of natural killer cell mediated cytotoxicity / Interleukin-3, Interleukin-5 and GM-CSF signaling / FCERI mediated Ca+2 mobilization / Regulation of actin dynamics for phagocytic cup formation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFA-VEGFR2 Pathway / regulation of cell size / small GTPase mediated signal transduction / T cell differentiation / positive regulation of cell adhesion / phagocytosis / regulation of GTPase activity / T cell activation / reactive oxygen species metabolic process / guanyl-nucleotide exchange factor activity / phosphotyrosine residue binding / neutrophil chemotaxis / integrin-mediated signaling pathway / positive regulation of GTPase activity / cell-cell junction / cell migration / G protein-coupled receptor signaling pathway / immune response / intracellular signal transduction / metal ion binding / cytosol / cytoplasm
Similarity search - Function
VAV1 protein, second SH3 domain / Protein vav1 / VAV1, SH2 domain / VAV1 protein, first SH3 domain / Vav, PH domain / Smooth muscle protein/calponin / CAMSAP CH domain / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / Dbl homology (DH) domain signature. / Guanine-nucleotide dissociation stimulator, CDC24, conserved site ...VAV1 protein, second SH3 domain / Protein vav1 / VAV1, SH2 domain / VAV1 protein, first SH3 domain / Vav, PH domain / Smooth muscle protein/calponin / CAMSAP CH domain / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / Dbl homology (DH) domain signature. / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Phorbol esters/diacylglycerol binding domain (C1 domain) / RhoGEF domain / Dbl homology (DH) domain superfamily / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Calponin homology domain / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Calponin homology (CH) domain profile. / CH domain superfamily / Calponin homology domain / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / SH3 type barrels. / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsOgura, K. / Nagata, K. / Horiuchi, M. / Ebisui, E. / Hasuda, T. / Yuzawa, S. / Nishida, M. / Hatanaka, H. / Inagaki, F.
CitationJournal: J.BIOMOL.NMR / Year: 2002
Title: Solution structure of N-terminal SH3 domain of Vav and the recognition site for Grb2 C-terminal SH3 domain
Authors: Ogura, K. / Nagata, K. / Horiuchi, M. / Ebisui, E. / Hasuda, T. / Yuzawa, S. / Nishida, M. / Hatanaka, H. / Inagaki, F.
History
DepositionSep 26, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: 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

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Assembly

Deposited unit
A: vav


Theoretical massNumber of molelcules
Total (without water)8,9901
Polymers8,9901
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: Protein vav / VAV proto-oncogene


Mass: 8990.082 Da / Num. of mol.: 1 / Fragment: N-terminal SH3 domain / Mutation: P33G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pHT-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P27870

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2223D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 1.5mM protein U-15N,13C; 10mM phosphate buffer K; 10mM DTT-d
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.8 / Pressure: 1 atm / Temperature: 298 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1Nilgesstructure solution
ARIA1Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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