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- PDB-2lnx: Solution structure of Vav2 SH2 domain -

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Basic information

Entry
Database: PDB / ID: 2lnx
TitleSolution structure of Vav2 SH2 domain
ComponentsGuanine nucleotide exchange factor VAV2
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


Azathioprine ADME / regulation of small GTPase mediated signal transduction / lamellipodium assembly / regulation of cell size / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / regulation of GTPase activity / Fc-gamma receptor signaling pathway involved in phagocytosis ...Azathioprine ADME / regulation of small GTPase mediated signal transduction / lamellipodium assembly / regulation of cell size / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / regulation of GTPase activity / Fc-gamma receptor signaling pathway involved in phagocytosis / 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 / guanyl-nucleotide exchange factor activity / VEGFR2 mediated vascular permeability / Signal transduction by L1 / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / platelet activation / 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. / Variant SH3 domain / Calponin homology 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. / 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. / 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 / 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
Guanine nucleotide exchange factor VAV2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, B. / Zhang, J. / Wu, J. / Shi, Y.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Identification and structural basis for a novel interaction between Vav2 and Arap3.
Authors: Wu, B. / Wang, F. / Zhang, J. / Zhang, Z. / Qin, L. / Peng, J. / Li, F. / Liu, J. / Lu, G. / Gong, Q. / Yao, X. / Wu, J. / Shi, Y.
History
DepositionJan 5, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanine nucleotide exchange factor VAV2


Theoretical massNumber of molelcules
Total (without water)14,6291
Polymers14,6291
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Guanine nucleotide exchange factor VAV2 / VAV-2


Mass: 14628.519 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 659-771
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAV2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52735

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D HCACO
1613D C(CO)NH
1713D H(CCO)NH
1813D HBHA(CO)NH
1913D 1H-15N NOESY
11023D (H)CCH-TOCSY
11123D (H)CCH-COSY
11223D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N] entity-1, 5 mM DTT-2, 75 mM sodium chloride-3, 5 mM potassium phosphate-4, 20 mM sodium phosphate-5, 1 mM EDTA-6, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] entity-7, 75 mM sodium chloride-8, 5 mM DTT-9, 5 mM potassium phosphate-10, 20 mM sodium phosphate-11, 1 mM EDTA-12, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-1[U-13C; U-15N]1
5 mMDTT-21
75 mMsodium chloride-31
5 mMpotassium phosphate-41
20 mMsodium phosphate-51
1 mMEDTA-61
1 mMentity-7[U-13C; U-15N]2
75 mMsodium chloride-82
5 mMDTT-92
5 mMpotassium phosphate-102
20 mMsodium phosphate-112
1 mMEDTA-122
Sample conditionsIonic strength: 120 / pH: 6.2 / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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