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- PDB-2crh: Solution structure of the SH2 domain of human proto-oncogene prot... -

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Basic information

Entry
Database: PDB / ID: 2crh
TitleSolution structure of the SH2 domain of human proto-oncogene protein VAV1
ComponentsVav proto-oncogene
KeywordsSIGNALING PROTEIN / ONCOPROTEIN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


phosphorylation-dependent protein binding / positive regulation of natural killer cell mediated cytotoxicity / Azathioprine ADME / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / natural killer cell mediated cytotoxicity / Fc-gamma receptor signaling pathway involved in phagocytosis / NRAGE signals death through JNK / regulation of cell size / regulation of GTPase activity ...phosphorylation-dependent protein binding / positive regulation of natural killer cell mediated cytotoxicity / Azathioprine ADME / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / natural killer cell mediated cytotoxicity / Fc-gamma receptor signaling pathway involved in phagocytosis / NRAGE signals death through JNK / regulation of cell size / regulation of GTPase activity / Fc-epsilon receptor signaling pathway / Interleukin-3, Interleukin-5 and GM-CSF signaling / T cell differentiation / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / vascular endothelial growth factor receptor signaling pathway / Erythropoietin activates RAS / GPVI-mediated activation cascade / T cell costimulation / phosphotyrosine residue binding / neutrophil chemotaxis / RAC1 GTPase cycle / FCERI mediated Ca+2 mobilization / reactive oxygen species metabolic process / VEGFR2 mediated vascular permeability / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / guanyl-nucleotide exchange factor activity / integrin-mediated signaling pathway / Regulation of signaling by CBL / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Signaling by SCF-KIT / platelet activation / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / Constitutive Signaling by Aberrant PI3K in Cancer / cell-cell junction / G alpha (12/13) signalling events / cell migration / cellular response to xenobiotic stimulus / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Potential therapeutics for SARS / intracellular signal transduction / G protein-coupled receptor signaling pathway / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
VAV1 protein, second SH3 domain / VAV1 protein, first SH3 domain / VAV1, SH2 domain / Vav, PH domain / Smooth muscle protein/calponin / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Calponin homology domain ...VAV1 protein, second SH3 domain / VAV1 protein, first SH3 domain / VAV1, SH2 domain / Vav, PH domain / Smooth muscle protein/calponin / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Calponin homology domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / SH2 domain / SHC Adaptor Protein / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / 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 / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsEndo, H. / Hayashi, F. / Yoshida, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: Solution structure of the SH2 domain of human proto-oncogene protein VAV1
Authors: Endo, H. / Hayashi, F. / Yoshida, M. / Yokoyama, S.
History
DepositionMay 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vav proto-oncogene


Theoretical massNumber of molelcules
Total (without water)15,4961
Polymers15,4961
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, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Vav proto-oncogene


Mass: 15496.418 Da / Num. of mol.: 1 / Fragment: SH2 (residues 1-138)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: VAV1, VAV / Plasmid: P040517-08 / References: UniProt: P15498

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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

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Sample preparation

DetailsContents: 1.15mM 13C,15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20031121Delaglio,F.processing
NMRView5.0.4Johnson,B.A.data analysis
KUJIRA0.9296Kobayashi,N.data analysis
CYANA2.0.17Guntert,P.structure solution
CYANA2.0.17Guntert,P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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