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- PDB-2ror: Solution structure of the VAV1 SH2 domain complexed with a tyrosi... -

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Basic information

Entry
Database: PDB / ID: 2ror
TitleSolution structure of the VAV1 SH2 domain complexed with a tyrosine-phosphorylated peptide from SLP76
Components
  • 15-meric peptide from Lymphocyte cytosolic protein 2
  • Proto-oncogene vav
KeywordsSIGNALING PROTEIN / SH2 domain / protein-peptide complex / phosphorylated peptide recognition / phosphotyrosine binding domain / signal transduction / Guanine-nucleotide releasing factor / Metal-binding / Phorbol-ester binding / Phosphoprotein / Proto-oncogene / SH3 domain / Zinc / Zinc-finger / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


TCR signalosome / mast cell activation / phosphorylation-dependent protein binding / Azathioprine ADME / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / regulation of cell size / NRAGE signals death through JNK / positive regulation of natural killer cell mediated cytotoxicity / regulation of GTPase activity ...TCR signalosome / mast cell activation / phosphorylation-dependent protein binding / Azathioprine ADME / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / regulation of cell size / NRAGE signals death through JNK / positive regulation of natural killer cell mediated cytotoxicity / regulation of GTPase activity / Fc-gamma receptor signaling pathway involved in phagocytosis / Fc-epsilon receptor signaling pathway / plasma membrane raft / Generation of second messenger molecules / RHOG GTPase cycle / T cell differentiation / RHOA GTPase cycle / Interleukin-3, Interleukin-5 and GM-CSF signaling / RAC2 GTPase cycle / positive regulation of protein kinase activity / vascular endothelial growth factor receptor signaling pathway / Erythropoietin activates RAS / GPVI-mediated activation cascade / RAC1 GTPase cycle / T cell costimulation / reactive oxygen species metabolic process / phosphotyrosine residue binding / FCERI mediated Ca+2 mobilization / guanyl-nucleotide exchange factor activity / neutrophil chemotaxis / VEGFR2 mediated vascular permeability / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / integrin-mediated signaling pathway / Regulation of signaling by CBL / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Signaling by SCF-KIT / Regulation of actin dynamics for phagocytic cup formation / platelet activation / VEGFA-VEGFR2 Pathway / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / G alpha (12/13) signalling events / cell-cell junction / cell migration / cellular response to xenobiotic stimulus / PIP3 activates AKT signaling / DAP12 signaling / T cell receptor signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Potential therapeutics for SARS / intracellular signal transduction / immune response / 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) / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / 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. / SH2 domain / Zinc finger phorbol-ester/DAG-type signature. / SHC Adaptor Protein / 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 / SAM domain (Sterile alpha motif) / Sterile alpha motif. / Sterile alpha motif domain / PH domain / Sterile alpha motif/pointed domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains / SH2 domain / 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
Proto-oncogene vav / Lymphocyte cytosolic protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTanaka, M. / Kasai, T. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the VAV1 SH2 domain complexed with a tyrosine-phosphorylated peptide from SLP76
Authors: Kasai, T. / Tanaka, M. / Koshiba, S. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 8, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proto-oncogene vav
B: 15-meric peptide from Lymphocyte cytosolic protein 2


Theoretical massNumber of molelcules
Total (without water)17,2902
Polymers17,2902
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Proto-oncogene vav


Mass: 15496.418 Da / Num. of mol.: 1 / Fragment: SH2 domain, UNP residues 629-775
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: E. coli cell free / Gene: VAV1 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: P15498
#2: Protein/peptide 15-meric peptide from Lymphocyte cytosolic protein 2 / SH2 domain-containing leukocyte protein of 76 kDa / SLP-76 tyrosine phosphoprotein / SLP76


Mass: 1793.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / References: UniProt: Q13094
Sequence detailsTHIS PROTEIN HAS A DELETION REGION AGAINST THE DATABASE REFERENCE, VAV_HUMAN. THE DEPOSITOR BELIEVE ...THIS PROTEIN HAS A DELETION REGION AGAINST THE DATABASE REFERENCE, VAV_HUMAN. THE DEPOSITOR BELIEVE THAT THIS PROTEIN IS A VARIANT, EVEN THOUGH IT HAS NOT BEEN REFERRED IN ANY DATABASES.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1313D F1-15N,13C-filtered 15N-separated NOESY
1413D F1-15N,13C-filtered 13C-separated NOESY
1512D F2-15N,13C-filtered NOESY

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Sample preparation

DetailsContents: 1.08mM [U-13C; U-15N] Proto-oncogene vav; 1.08mM tyrosine-phosphorylated peptide; 20mM [U-2H] TRIS; 100mM sodium chloride; 0.02% sodium azide; 1mM [U-2H] DTT; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.08 mMentity_1[U-13C; U-15N]1
1.08 mMentity_21
20 mMTRIS[U-2H]1
100 mMsodium chloride1
0.02 %sodium azide1
1 mMDTT[U-2H]1
Sample conditionsIonic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.6Bruker Biospincollection
NMRPipe2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.0.4Johnson, One Moon Scientificdata analysis
NMRView5.0.4Johnson, One Moon Scientificpeak picking
NMRView5.0.4Johnson, One Moon Scientificchemical shift assignment
KUJIRA0.9837Kobayashi, N.data analysis
KUJIRA0.9837Kobayashi, N.peak picking
KUJIRA0.9837Kobayashi, N.chemical shift assignment
CYANA2.0.17Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.0.17Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2918 / NOE intraresidue total count: 686 / NOE long range total count: 945 / NOE medium range total count: 443 / NOE sequential total count: 741 / Protein chi angle constraints total count: 122 / Protein other angle constraints total count: 94 / Protein phi angle constraints total count: 172 / Protein psi angle constraints total count: 172
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 6.94 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 10.43 ° / Maximum upper distance constraint violation: 0.48 Å
NMR ensemble rmsDistance rms dev: 0.0047 Å

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