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- PDB-1gcq: CRYSTAL STRUCTURE OF VAV AND GRB2 SH3 DOMAINS -

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Basic information

Entry
Database: PDB / ID: 1gcq
TitleCRYSTAL STRUCTURE OF VAV AND GRB2 SH3 DOMAINS
Components
  • GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
  • VAV PROTO-ONCOGENE
KeywordsSIGNALING PROTEIN/SIGNALING PROTEIN / SH3 domain / PROTEIN-PROTEIN COMPLEX / Grb2 / Vav / SIGNALING PROTEIN-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


Azathioprine ADME / CD28 dependent Vav1 pathway / Erythropoietin activates RAS / RAC2 GTPase cycle / GPVI-mediated activation cascade / FCERI mediated MAPK activation / NRAGE signals death through JNK / Signaling by SCF-KIT / guanyl-nucleotide exchange factor adaptor activity / VEGFR2 mediated vascular permeability ...Azathioprine ADME / CD28 dependent Vav1 pathway / Erythropoietin activates RAS / RAC2 GTPase cycle / GPVI-mediated activation cascade / FCERI mediated MAPK activation / NRAGE signals death through JNK / Signaling by SCF-KIT / guanyl-nucleotide exchange factor adaptor activity / VEGFR2 mediated vascular permeability / RAC1 GTPase cycle / Grb2-EGFR complex / G alpha (12/13) signalling events / FCERI mediated Ca+2 mobilization / PIP3 activates AKT signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / RHOA GTPase cycle / Regulation of signaling by CBL / RHOG GTPase cycle / phosphorylation-dependent protein binding / Regulation of actin dynamics for phagocytic cup formation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / positive regulation of natural killer cell mediated cytotoxicity / Co-inhibition by BTLA / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / MET receptor recycling / VEGFA-VEGFR2 Pathway / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / MET activates PTPN11 / negative regulation of natural killer cell mediated cytotoxicity / MET activates RAP1 and RAC1 / natural killer cell activation / vesicle membrane / Signaling by LTK / CD28 dependent Vav1 pathway / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / epidermal growth factor receptor binding / Regulation of KIT signaling / PI-3K cascade:FGFR3 / natural killer cell mediated cytotoxicity / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / regulation of cell size / positive regulation of actin filament polymerization / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / regulation of MAPK cascade / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / PI3K events in ERBB2 signaling / insulin receptor substrate binding / T cell differentiation / signal transduction in response to DNA damage / SOS-mediated signalling / fibroblast growth factor receptor signaling pathway / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / Role of LAT2/NTAL/LAB on calcium mobilization / SHC1 events in ERBB4 signaling / Interleukin receptor SHC signaling / RHO GTPases Activate WASPs and WAVEs / GAB1 signalosome / Signalling to RAS / Signal attenuation / phagocytosis / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Schwann cell development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / ephrin receptor binding / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / T cell costimulation / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / Signaling by FGFR2 in disease
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 / GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like ...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 / GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Calponin homology 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. / Phorbol esters/diacylglycerol binding domain (C1 domain) / 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 / 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 / SH3 type barrels. / 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
Proto-oncogene vav / Growth factor receptor-bound protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.68 Å
AuthorsNishida, M. / Nagata, K. / Hachimori, Y. / Ogura, K. / Inagaki, F.
CitationJournal: EMBO J. / Year: 2001
Title: Novel recognition mode between Vav and Grb2 SH3 domains.
Authors: Nishida, M. / Nagata, K. / Hachimori, Y. / Horiuchi, M. / Ogura, K. / Mandiyan, V. / Schlessinger, J. / Inagaki, F.
History
DepositionAug 8, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
B: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
C: VAV PROTO-ONCOGENE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1454
Polymers22,0273
Non-polymers1181
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.050, 126.820, 83.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2


Mass: 6998.661 Da / Num. of mol.: 2 / Fragment: C-TERMINAL SH3 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P62993
#2: Protein VAV PROTO-ONCOGENE


Mass: 8029.990 Da / Num. of mol.: 1 / Fragment: N-TERMINAL SH3 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: HEMATOPOIETIC CELLS / Plasmid: PET28A(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P27870
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2-methyl-2,4-pentanediol, imidazole, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.5 mMVavS1drop
23.0 mMGrbS1drop
3100 mMimidazole1reservoir
467 %(v/v)MPD1reservoir
575 mM1reservoirMgCl2
61 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.0375
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0375 Å / Relative weight: 1
ReflectionResolution: 1.68→39.5 Å / Num. all: 28649 / Num. obs: 28649 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -10000 / Redundancy: 10.3 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.2
Reflection shellResolution: 1.68→1.77 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.199 / Num. unique all: 3523 / % possible all: 83.9
Reflection
*PLUS
Num. measured all: 293792

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.68→8 Å / SU B: 19.1 / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1358 5 %RANDOM
Rwork0.201 ---
all0.207 28127 --
obs0.203 27162 93.1 %-
Displacement parametersBiso mean: 19.1 Å2
Refinement stepCycle: LAST / Resolution: 1.68→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1481 0 0 197 1678
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.395
X-RAY DIFFRACTIONx_dihedral_angle_d27.7
X-RAY DIFFRACTIONx_improper_angle_d1.27
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.27
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5

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