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- PDB-6new: Apo structure of the activated truncation of Vav1 -

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Basic information

Entry
Database: PDB / ID: 6new
TitleApo structure of the activated truncation of Vav1
ComponentsProto-oncogene vav
KeywordsMETAL BINDING PROTEIN / GEF / Rac / Vav1
Function / homology
Function and homology information


phosphorylation-dependent protein binding / Azathioprine ADME / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / regulation of cell size / regulation of GTPase activity / NRAGE signals death through JNK / positive regulation of natural killer cell mediated cytotoxicity / Fc-gamma receptor signaling pathway involved in phagocytosis / Fc-epsilon receptor signaling pathway ...phosphorylation-dependent protein binding / Azathioprine ADME / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / regulation of cell size / regulation of GTPase activity / NRAGE signals death through JNK / positive regulation of natural killer cell mediated cytotoxicity / Fc-gamma receptor signaling pathway involved in phagocytosis / Fc-epsilon receptor signaling pathway / RHOG GTPase cycle / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / RHOA GTPase cycle / RAC2 GTPase cycle / 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 / 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 / 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. / 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 / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsKnapp, M.S. / Elling, R.A. / Ornelas, E.
CitationJournal: To Be Published
Title: Allosteric Inhibitors of VAV1 Block Guanine Nucleotide Exchange Activity
Authors: Gerspacher, M. / Skaanderup, P.R.
History
DepositionDec 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proto-oncogene vav
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8113
Polymers49,6801
Non-polymers1312
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.925, 67.693, 178.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Proto-oncogene vav / Vav1 vav guanine nucleotide exchange factor 1


Mass: 49679.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAV1, VAV / Production host: Escherichia coli (E. coli) / References: UniProt: P15498
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 16-22% (v/v) Ethylene Glycol, 0.1M TRIS pH 7.3, and 15% (w/v) Polyethylene Glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.5→44.7 Å / Num. obs: 16248 / % possible obs: 99.9 % / Redundancy: 14.1 % / Biso Wilson estimate: 50.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.032 / Rrim(I) all: 0.12 / Net I/σ(I): 22 / Num. measured all: 228443 / Scaling rejects: 1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.74 / Num. unique obs: 1770 / CC1/2: 0.916 / Rpim(I) all: 0.199 / Rrim(I) all: 0.767 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6 Å44.7 Å
Translation6 Å44.7 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.29data scaling
PHASER2.7.17phasing
BUSTERrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house Vav1-Rac1 complex

Resolution: 2.5→44.7 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.877 / SU R Cruickshank DPI: 0.526 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.714 / SU Rfree Blow DPI: 0.298 / SU Rfree Cruickshank DPI: 0.29
RfactorNum. reflection% reflectionSelection details
Rfree0.257 797 4.92 %RANDOM
Rwork0.199 ---
obs0.202 16198 99.7 %-
Displacement parametersBiso max: 180.23 Å2 / Biso mean: 58.13 Å2 / Biso min: 15.09 Å2
Baniso -1Baniso -2Baniso -3
1-8.0431 Å20 Å20 Å2
2--1.1026 Å20 Å2
3----9.1457 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.5→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 2 195 3303
Biso mean--34.1 50.32 -
Num. residues----389
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1152SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes464HARMONIC5
X-RAY DIFFRACTIONt_it3174HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion406SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3557SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3174HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4271HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion18.55
LS refinement shellResolution: 2.5→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2957 134 4.72 %
Rwork0.2242 2703 -
all0.2274 2837 -
obs--99.51 %
Refinement TLS params.Method: refined / Origin x: 18.419 Å / Origin y: 74.991 Å / Origin z: 24.3618 Å
111213212223313233
T-0.0114 Å20.0635 Å20.0051 Å2--0.2303 Å2-0.037 Å2---0.1912 Å2
L0.5554 °2-0.1316 °20.4723 °2-1.4198 °20.6644 °2--2.8338 °2
S0.1319 Å °0.2447 Å °0.0404 Å °-0.1261 Å °-0.0098 Å °-0.1771 Å °0.5442 Å °0.1949 Å °-0.122 Å °
Refinement TLS groupSelection details: { A|* }

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