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- PDB-2dm1: Solution structure of the second SH3 domain of human protein vav-2 -

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Basic information

Entry
Database: PDB / ID: 2dm1
TitleSolution structure of the second SH3 domain of human protein vav-2
ComponentsProtein vav-2
KeywordsSIGNALING PROTEIN / Rho family Guanine nucleotide exchange factor / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Azathioprine ADME / regulation of small GTPase mediated signal transduction / lamellipodium assembly / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / regulation of cell size / regulation of GTPase activity / RHOB GTPase cycle / Fc-gamma receptor signaling pathway involved in phagocytosis / NRAGE signals death through JNK ...Azathioprine ADME / regulation of small GTPase mediated signal transduction / lamellipodium assembly / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / regulation of cell size / regulation of GTPase activity / RHOB GTPase cycle / Fc-gamma receptor signaling pathway involved in phagocytosis / NRAGE signals death through JNK / RHOC GTPase cycle / Fc-epsilon receptor signaling pathway / CDC42 GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / vascular endothelial growth factor receptor signaling pathway / GPVI-mediated activation cascade / RAC1 GTPase cycle / phosphotyrosine residue binding / FCERI mediated Ca+2 mobilization / VEGFR2 mediated vascular permeability / guanyl-nucleotide exchange factor activity / Signal transduction by L1 / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / platelet activation / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / G alpha (12/13) signalling events / cell migration / cellular response to xenobiotic stimulus / DAP12 signaling / angiogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / signal transduction / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
VAV2 protein, second SH3 domain / VAV2 protein, first SH3 domain / VAV2, SH2 domain / Vav, PH domain / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / SOS1/NGEF-like PH domain / Variant SH3 domain ...VAV2 protein, second SH3 domain / VAV2 protein, first SH3 domain / VAV2, SH2 domain / Vav, PH domain / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / SOS1/NGEF-like PH domain / Variant SH3 domain / 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. / 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 / SH3 Domains / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / 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 / Roll / Mainly Beta
Similarity search - Domain/homology
Guanine nucleotide exchange factor VAV2
Similarity search - Component
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 second SH3 domain of human protein vav-2
Authors: Endo, H. / Hayashi, F. / Yoshida, M. / Yokoyama, S.
History
DepositionApr 20, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2007Provider: 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _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

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Assembly

Deposited unit
A: Protein vav-2


Theoretical massNumber of molelcules
Total (without water)7,8521
Polymers7,8521
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 Protein vav-2


Mass: 7852.479 Da / Num. of mol.: 1 / Fragment: sh3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: VAV2 / Plasmid: P050620-03 / References: UniProt: P52735

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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: 1.07mM 13C,15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.955Kobayashi, 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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