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- PDB-1gcp: CRYSTAL STRUCTURE OF VAV SH3 DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1gcp
TitleCRYSTAL STRUCTURE OF VAV SH3 DOMAIN
ComponentsVAV PROTO-ONCOGENE
KeywordsSIGNALING PROTEIN / SH3 DOMAIN / VAV
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 / VEGFR2 mediated vascular permeability / RAC1 GTPase cycle ...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 / VEGFR2 mediated vascular permeability / RAC1 GTPase cycle / 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 / positive regulation of natural killer cell mediated cytotoxicity / VEGFA-VEGFR2 Pathway / natural killer cell activation / natural killer cell mediated cytotoxicity / regulation of cell size / T cell differentiation / phagocytosis / T cell costimulation / phosphotyrosine residue binding / neutrophil chemotaxis / positive regulation of cell adhesion / reactive oxygen species metabolic process / guanyl-nucleotide exchange factor activity / T cell activation / integrin-mediated signaling pathway / cell-cell junction / intracellular signal transduction / immune response / G protein-coupled receptor signaling pathway / zinc ion binding / cytosol
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 / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.1 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 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VAV PROTO-ONCOGENE
B: VAV PROTO-ONCOGENE
C: VAV PROTO-ONCOGENE
D: VAV PROTO-ONCOGENE


Theoretical massNumber of molelcules
Total (without water)32,1204
Polymers32,1204
Non-polymers00
Water3,423190
1
A: VAV PROTO-ONCOGENE


Theoretical massNumber of molelcules
Total (without water)8,0301
Polymers8,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VAV PROTO-ONCOGENE


Theoretical massNumber of molelcules
Total (without water)8,0301
Polymers8,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: VAV PROTO-ONCOGENE


Theoretical massNumber of molelcules
Total (without water)8,0301
Polymers8,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: VAV PROTO-ONCOGENE


Theoretical massNumber of molelcules
Total (without water)8,0301
Polymers8,0301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.205, 101.115, 39.707
Angle α, β, γ (deg.)90.00, 91.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
VAV PROTO-ONCOGENE


Mass: 8029.990 Da / Num. of mol.: 4 / Fragment: N-TERMINAL 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.02 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 277.2 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG4000, tris(hydroxymethyl)aminomethane, isopropanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.0 mMprotein1drop
2100 mMTris-HCl1reservoir
330 %(w/v)PEG40001reservoir
49 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→8 Å / Num. all: 14004 / Num. obs: 14004 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 34.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.078 / Num. unique all: 1048 / % possible all: 70.7
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 84381

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: molecular replacement
Starting model: Vav SH3 domain in 1GCQ

1gcq


Resolution: 2.1→8 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 680 5 %RANDOM
Rwork0.193 ---
all0.198 13692 --
obs0.196 13606 93.4 %-
Displacement parametersBiso mean: 12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 0 190 2341
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.562
X-RAY DIFFRACTIONx_dihedral_angle_d28.26
X-RAY DIFFRACTIONx_improper_angle_d1.54
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
Highest resolution: 2.1 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.54
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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