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- PDB-2lct: Solution structure of the Vav1 SH2 domain complexed with a Syk-de... -

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Basic information

Entry
Database: PDB / ID: 2lct
TitleSolution structure of the Vav1 SH2 domain complexed with a Syk-derived doubly phosphorylated peptide
Components
  • Proto-oncogene vav
  • Tyrosine-protein kinase SYK
KeywordsSIGNALING PROTEIN / Phosphopeptide / Syk kinase / tyrosine kinase / protein-peptide complex / phosphorylated peptide / phosphotyrosine binding domain / B cell signaling protein
Function / homology
Function and homology information


FLT3 signaling through SRC family kinases / Interleukin-2 signaling / serotonin secretion / Fc epsilon receptor (FCERI) signaling / Dectin-2 family / Signaling by CSF3 (G-CSF) / Role of LAT2/NTAL/LAB on calcium mobilization / GPVI-mediated activation cascade / FCERI mediated MAPK activation / Inactivation of CSF3 (G-CSF) signaling ...FLT3 signaling through SRC family kinases / Interleukin-2 signaling / serotonin secretion / Fc epsilon receptor (FCERI) signaling / Dectin-2 family / Signaling by CSF3 (G-CSF) / Role of LAT2/NTAL/LAB on calcium mobilization / GPVI-mediated activation cascade / FCERI mediated MAPK activation / Inactivation of CSF3 (G-CSF) signaling / FCGR activation / Role of phospholipids in phagocytosis / Integrin signaling / FCERI mediated Ca+2 mobilization / interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / cellular response to lectin / gamma-delta T cell differentiation / serotonin secretion by platelet / positive regulation of interleukin-3 production / positive regulation of gamma-delta T cell differentiation / phosphorylation-dependent protein binding / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Toll-like receptor binding / Regulation of signaling by CBL / regulation of platelet aggregation / Regulation of actin dynamics for phagocytic cup formation / positive regulation of alpha-beta T cell proliferation / leukocyte activation involved in immune response / neutrophil activation involved in immune response / positive regulation of mast cell cytokine production / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of mast cell degranulation / lymph vessel development / regulation of platelet activation / collagen-activated tyrosine kinase receptor signaling pathway / cell activation / positive regulation of killing of cells of another organism / regulation of phagocytosis / beta selection / macrophage activation involved in immune response / cellular response to molecule of fungal origin / early phagosome / leukotriene biosynthetic process / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of monocyte chemotactic protein-1 production / interleukin-3-mediated signaling pathway / cellular response to lipid / positive regulation of cell adhesion mediated by integrin / Azathioprine ADME / regulation of small GTPase mediated signal transduction / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of alpha-beta T cell differentiation / blood vessel morphogenesis / CD28 dependent Vav1 pathway / DAP12 signaling / natural killer cell mediated cytotoxicity / T cell receptor complex / positive regulation of B cell differentiation / leukocyte cell-cell adhesion / regulation of cell size / regulation of GTPase activity / mast cell degranulation / Fc-gamma receptor signaling pathway involved in phagocytosis / NRAGE signals death through JNK / enzyme-linked receptor protein signaling pathway / positive regulation of interleukin-4 production / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / phospholipase binding / positive regulation of receptor internalization / positive regulation of interleukin-10 production / cellular response to low-density lipoprotein particle stimulus / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / RHOG GTPase cycle / RHOA GTPase cycle / regulation of immune response / positive regulation of type I interferon production / RAC2 GTPase cycle / positive regulation of bone resorption / phosphatase binding / vascular endothelial growth factor receptor signaling pathway / Erythropoietin activates RAS / cell surface receptor protein tyrosine kinase signaling pathway / GPVI-mediated activation cascade / T cell costimulation / RAC1 GTPase cycle / positive regulation of TORC1 signaling / positive regulation of interleukin-12 production / positive regulation of calcium-mediated signaling / neutrophil chemotaxis / phosphotyrosine residue binding / reactive oxygen species metabolic process / FCERI mediated Ca+2 mobilization / SH2 domain binding / B cell differentiation
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 / Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 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 / Tyrosine-protein kinase, non-receptor SYK/ZAP-70 / Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain superfamily / SYK/ZAP-70, N-terminal SH2 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 / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Proto-oncogene vav / Tyrosine-protein kinase SYK
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsChen, C. / Gorenstein, N. / Post, C.
CitationJournal: Mol.Cell.Biol. / Year: 2011
Title: Two closely spaced tyrosines regulate NFAT signaling in B cells via Syk association with Vav.
Authors: Chen, C.H. / Martin, V.A. / Gorenstein, N.M. / Geahlen, R.L. / Post, C.B.
History
DepositionMay 9, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_database_status.status_code_nmr_data / _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

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Assembly

Deposited unit
A: Proto-oncogene vav
B: Tyrosine-protein kinase SYK


Theoretical massNumber of molelcules
Total (without water)14,0102
Polymers14,0102
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 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Proto-oncogene vav


Mass: 12335.144 Da / Num. of mol.: 1 / Fragment: SH2 domain residues 664-767
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAV, VAV1 / Production host: Escherichia coli (E. coli) / References: UniProt: P15498
#2: Protein/peptide Tyrosine-protein kinase SYK / Spleen tyrosine kinase


Mass: 1674.458 Da / Num. of mol.: 1 / Fragment: sequence database residues 338-350 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
References: UniProt: P48025, non-specific protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HN(CA)CB
1313D HNCA
1413D HN(CO)CA
1513D HBHA(CO)NH
1613D (H)CCH-TOCSY
1713D C(CO)NH
1813D H(CCO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D 1H-13C NOESY aromatic
11212D 1H-13C HSQC aromatic
11312D 1H-1H TOCSY
11412D 1H-1H NOESY
1151single X-filtered NOESY
1161double X-filtered NOESY
1171double X-filtered TOCSY

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Sample preparation

DetailsContents: 1.1 mM [U-13C; U-15N] protein, 20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 0.02 % sodium azide, 1.1 mM peptide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMprotein_1-1[U-13C; U-15N]1
20 mMTRIS-21
100 mMsodium chloride-31
1 mMDTT-41
0.02 %sodium azide-51
1.1 mMprotein_2-61
Sample conditionsIonic strength: 120 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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