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Entry
Database: PDB / ID: 3bji
TitleStructural Basis of Promiscuous Guanine Nucleotide Exchange by the T-Cell Essential Vav1
Components
  • Proto-oncogene vav
  • Ras-related C3 botulinum toxin substrate 1 precursor
KeywordsSIGNALING PROTEIN / protein-protein interaction / GEF/GTPase / atypical cysteine rich domain / Guanine-nucleotide releasing factor / Metal-binding / Phorbol-ester binding / Phosphoprotein / Proto-oncogene / SH2 domain / SH3 domain / Zinc / Zinc-finger / ADP-ribosylation / Alternative splicing / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Polymorphism / Prenylation / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D
Function / homology
Function and homology information


regulation of respiratory burst / phosphorylation-dependent protein binding / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 ...regulation of respiratory burst / phosphorylation-dependent protein binding / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / engulfment of apoptotic cell / positive regulation of natural killer cell mediated cytotoxicity / WNT5:FZD7-mediated leishmania damping / respiratory burst / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / ruffle organization / thioesterase binding / regulation of stress fiber assembly / negative regulation of fibroblast migration / cell projection assembly / RHO GTPases activate CIT / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / PCP/CE pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / RHO GTPases activate KTN1 / Activation of RAC1 / motor neuron axon guidance / regulation of lamellipodium assembly / Azathioprine ADME / MET activates RAP1 and RAC1 / regulation of small GTPase mediated signal transduction / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / regulation of cell size / establishment or maintenance of cell polarity / DSCAM interactions / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / positive regulation of Rho protein signal transduction / regulation of GTPase activity / Fc-gamma receptor signaling pathway involved in phagocytosis / NRAGE signals death through JNK / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / Fc-epsilon receptor signaling pathway / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / RHOG GTPase cycle / RHOA GTPase cycle / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / localization / RHO GTPases activate IQGAPs / anatomical structure morphogenesis / vascular endothelial growth factor receptor signaling pathway / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / Erythropoietin activates RAS / positive regulation of substrate adhesion-dependent cell spreading / RHO GTPases activate PKNs / regulation of cell migration / positive regulation of microtubule polymerization / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / T cell costimulation / EPHB-mediated forward signaling / RAC1 GTPase cycle / actin filament polymerization / phosphotyrosine residue binding / positive regulation of endothelial cell migration / reactive oxygen species metabolic process / FCERI mediated Ca+2 mobilization / neutrophil chemotaxis / substrate adhesion-dependent cell spreading / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / cell chemotaxis / small monomeric GTPase / secretory granule membrane / VEGFR2 mediated vascular permeability / G protein activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
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 / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Dbl Homology Domain; Chain A / Dbl homology (DH) 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 / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Small GTPase Rho / small GTPase Rho family profile. / 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. / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / SH3 domain / Small GTPase / Ras family / Rab subfamily of small GTPases / 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 / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Proto-oncogene vav / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsChrencik, J.E. / Brooun, A. / Kuhn, P. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural basis of guanine nucleotide exchange mediated by the T-cell essential Vav1.
Authors: Chrencik, J.E. / Brooun, A. / Zhang, H. / Mathews, I.I. / Hura, G.L. / Foster, S.A. / Perry, J.J. / Streiff, M. / Ramage, P. / Widmer, H. / Bokoch, G.M. / Tainer, J.A. / Weckbecker, G. / Kuhn, P.
History
DepositionDec 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proto-oncogene vav
B: Proto-oncogene vav
C: Ras-related C3 botulinum toxin substrate 1 precursor
D: Ras-related C3 botulinum toxin substrate 1 precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6618
Polymers128,4004
Non-polymers2624
Water1,08160
1
A: Proto-oncogene vav
D: Ras-related C3 botulinum toxin substrate 1 precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3314
Polymers64,2002
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-14 kcal/mol
Surface area25360 Å2
MethodPISA
2
B: Proto-oncogene vav
C: Ras-related C3 botulinum toxin substrate 1 precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3314
Polymers64,2002
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-12 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.948, 75.079, 114.857
Angle α, β, γ (deg.)90.00, 103.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Proto-oncogene vav


Mass: 44489.082 Da / Num. of mol.: 2 / Fragment: Vav1 DH/PH/CRD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAV1, VAV / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (AI) / References: UniProt: P15498
#2: Protein Ras-related C3 botulinum toxin substrate 1 precursor / p21-Rac1 / Ras- like protein TC25 / Cell migration-inducing gene 5 protein


Mass: 19710.764 Da / Num. of mol.: 2 / Fragment: Rac1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: P63000
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 17% PEG-3350, 100 mM HEPES, pH 7.5, 200 mM ammonium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.95 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 1, 2006 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 36259 / Num. obs: 36156 / % possible obs: 100 % / Redundancy: 3 %
Reflection shellResolution: 2.6→2.667 Å / Num. unique all: 1861 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: 1FOE

1foe


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.873 / SU B: 12.481 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 1.127 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29253 1939 5.1 %RANDOM
Rwork0.2211 ---
obs0.22473 36156 100 %-
all-38095 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.506 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.1 Å2
2--0.06 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8359 0 4 60 8423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228550
X-RAY DIFFRACTIONr_bond_other_d0.0020.025686
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.95811577
X-RAY DIFFRACTIONr_angle_other_deg1.448313869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.02451076
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97224.241382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.201151428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3491547
X-RAY DIFFRACTIONr_chiral_restr0.2760.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029567
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021735
X-RAY DIFFRACTIONr_nbd_refined0.2430.22205
X-RAY DIFFRACTIONr_nbd_other0.2120.26017
X-RAY DIFFRACTIONr_nbtor_refined0.1940.24096
X-RAY DIFFRACTIONr_nbtor_other0.0970.24745
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2257
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0590.24
X-RAY DIFFRACTIONr_metal_ion_refined0.1690.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.350.27
X-RAY DIFFRACTIONr_mcbond_it0.6911.55550
X-RAY DIFFRACTIONr_mcbond_other0.0941.52180
X-RAY DIFFRACTIONr_mcangle_it1.1928624
X-RAY DIFFRACTIONr_scbond_it1.42833403
X-RAY DIFFRACTIONr_scangle_it2.3054.52953
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 105 -
Rwork0.258 1861 -
obs-36156 100 %

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