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- PDB-2mc1: Solution structure of the Vav1 SH2 domain complexed with a Syk-de... -

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Basic information

Entry
Database: PDB / ID: 2mc1
TitleSolution structure of the Vav1 SH2 domain complexed with a Syk-derived singly phosphorylated peptide
Components
  • Proto-oncogene vav
  • Tyrosine-protein kinase SYK
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / SYK KINASE / TYROSINE KINASE / PHOSPHORYLATED PEPTIDE / PHOSPHOTYROSINE BINDING DOMAIN / B CELL SIGNALING PROTEIN / SIGNALING PROTEIN-PROTEIN BINDING complex
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 / immune response-regulating cell surface receptor signaling pathway / Integrin signaling / FCERI mediated Ca+2 mobilization / interleukin-15 receptor binding / regulation of superoxide anion generation / regulation of neutrophil degranulation / regulation of arachidonate secretion / positive regulation of interleukin-3 production / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / cellular response to lectin / B cell receptor complex / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of signaling by CBL / regulation of platelet aggregation / Toll-like receptor binding / serotonin secretion by platelet / positive regulation of alpha-beta T cell proliferation / phosphorylation-dependent protein binding / leukocyte activation involved in immune response / Regulation of actin dynamics for phagocytic cup formation / positive regulation of mast cell cytokine production / neutrophil activation involved in immune response / cell surface pattern recognition receptor signaling pathway / positive regulation of mast cell degranulation / lymph vessel development / collagen-activated tyrosine kinase receptor signaling pathway / positive regulation of natural killer cell mediated cytotoxicity / regulation of platelet activation / cell activation / beta selection / cellular response to molecule of fungal origin / early phagosome / leukotriene biosynthetic process / regulation of phagocytosis / macrophage activation involved in immune response / regulation of tumor necrosis factor-mediated signaling pathway / interleukin-3-mediated signaling pathway / positive regulation of monocyte chemotactic protein-1 production / cellular response to lipid / natural killer cell activation / regulation of small GTPase mediated signal transduction / Azathioprine ADME / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of cell adhesion mediated by integrin / positive regulation of alpha-beta T cell differentiation / DAP12 signaling / CD28 dependent Vav1 pathway / blood vessel morphogenesis / regulation of GTPase activity / positive regulation of B cell differentiation / leukocyte cell-cell adhesion / T cell receptor complex / mast cell degranulation / natural killer cell mediated cytotoxicity / small GTPase-mediated signal transduction / NRAGE signals death through JNK / enzyme-linked receptor protein signaling pathway / regulation of cell size / positive regulation of interleukin-4 production / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase binding / amyloid-beta clearance / positive regulation of interleukin-10 production / positive regulation of receptor internalization / 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 / RAC2 GTPase cycle / positive regulation of type I interferon production / positive regulation of bone resorption / vascular endothelial growth factor receptor signaling pathway / phosphatase binding / regulation of ERK1 and ERK2 cascade / Erythropoietin activates RAS / GPVI-mediated activation cascade / T cell costimulation / RAC1 GTPase cycle / neutrophil chemotaxis / phosphotyrosine residue binding / positive regulation of interleukin-12 production / positive regulation of TORC1 signaling / FCERI mediated Ca+2 mobilization / 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 / SH2 domain superfamily / Src homology 3 domains / 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. / Tyrosine-protein kinase, active site / PH-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
AuthorsChen, C. / Piraner, D. / Gorenstein, N.M. / Geahlen, R.L. / Post, C.B.
CitationJournal: Biopolymers / Year: 2013
Title: Differential recognition of syk-binding sites by each of the two phosphotyrosine-binding pockets of the Vav SH2 domain.
Authors: Chen, C.H. / Piraner, D. / Gorenstein, N.M. / Geahlen, R.L. / Beth Post, C.
History
DepositionAug 13, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Oct 2, 2013Group: 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
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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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)13,9302
Polymers13,9302
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Proto-oncogene vav


Mass: 12335.144 Da / Num. of mol.: 1 / Fragment: SH2 domain (UNP residues 664-767)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAV1, VAV / Plasmid: PETTEV411 / Production host: Escherichia coli (E. coli) / References: UniProt: P15498
#2: Protein/peptide Tyrosine-protein kinase SYK / Spleen tyrosine kinase


Mass: 1594.479 Da / Num. of mol.: 1 / Fragment: UNP residues 338-350 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P48025
Has protein modificationY

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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 HN(CA)CB
1313D (H)CCH-TOCSY
1413D H(CCO)NH
1513D C(CO)NH
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D 1H-13C NOESY aromatic
1912D 1H-1H TOCSY
11012D 1H-1H NOESY

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] protein, 1 mM peptide, 20 mM TRIS, 100 mM sodium chloride, 1 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_1-1[U-99% 13C; U-99% 15N]1
1 mMentity_2-21
20 mMTRIS-31
100 mMsodium chloride-41
1 mMDTT-51
0.02 %sodium azide-61
Sample conditionsIonic strength: 120 / pH: 7 / Pressure: ambient / Temperature: 298 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
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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