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- PDB-1f5x: NMR STRUCTURE OF THE Y174 AUTOINHIBITED DBL HOMOLOGY DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1f5x
TitleNMR STRUCTURE OF THE Y174 AUTOINHIBITED DBL HOMOLOGY DOMAIN
ComponentsRHO-GEF VAV
KeywordsSIGNALING PROTEIN / 11 alpha-HELICES
Function / homology
Function and homology information


Azathioprine ADME / CD28 dependent Vav1 pathway / RAC2 GTPase cycle / Erythropoietin activates RAS / GPVI-mediated activation cascade / RHOA GTPase cycle / FCERI mediated MAPK activation / NRAGE signals death through JNK / Signaling by SCF-KIT / RAC1 GTPase cycle ...Azathioprine ADME / CD28 dependent Vav1 pathway / RAC2 GTPase cycle / Erythropoietin activates RAS / GPVI-mediated activation cascade / RHOA GTPase cycle / FCERI mediated MAPK activation / NRAGE signals death through JNK / Signaling by SCF-KIT / RAC1 GTPase cycle / RHOG GTPase cycle / VEGFR2 mediated vascular permeability / FCERI mediated Ca+2 mobilization / phosphorylation-dependent protein binding / G alpha (12/13) signalling events / PIP3 activates AKT signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of signaling by CBL / Regulation of actin dynamics for phagocytic cup formation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / VEGFA-VEGFR2 Pathway / regulation of cell size / positive regulation of natural killer cell mediated cytotoxicity / T cell differentiation / positive regulation of cell adhesion / phagocytosis / reactive oxygen species metabolic process / phosphotyrosine residue binding / T cell activation / guanyl-nucleotide exchange factor activity / neutrophil chemotaxis / integrin-mediated signaling pathway / cell-cell junction / cell migration / intracellular signal transduction / immune response / G protein-coupled receptor signaling pathway / metal ion binding / 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 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site ...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 / Dbl Homology Domain; Chain A / Dbl homology (DH) 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAghazadeh, B. / Rosen, M.K. / Lowry, W.E. / Huang, X.Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structural basis for relief of autoinhibition of the Dbl homology domain of proto-oncogene Vav by tyrosine phosphorylation.
Authors: Aghazadeh, B. / Lowry, W.E. / Huang, X.Y. / Rosen, M.K.
History
DepositionJun 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RHO-GEF VAV


Theoretical massNumber of molelcules
Total (without water)24,4901
Polymers24,4901
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #16closest to the average

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Components

#1: Protein RHO-GEF VAV


Mass: 24490.309 Da / Num. of mol.: 1 / Fragment: DBL HOMOLOGY DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: P27870

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C-separated NOESY
1214D 13C/15N-separated NOESY
1313D 15N-separated NOESY
1413D 13C-separated NOESY
1512D NOESY
NMR detailsText: This structure was determined using 3D and 4D heteronuclear techniques on deuterated samples in conjunction with selective methyl and aromatic labeling

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Sample preparation

DetailsContents: 1.4 mM 15N,13C,2H; 20 mM phosphate buffer; 50 mM NaCl; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 70 mM / pH: 7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR2Variancollection
NMRPipe2Delaglioprocessing
NMRView2.1.2Johnsondata analysis
CNS0.3Brungerstructure solution
ARIA1Nilgesrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: CNS was used in the initial global fold determination. High-resolution structures were obtained using ARIA. Final structures are based on a total of 3966 restraints, 3523 are NOE-derived ...Details: CNS was used in the initial global fold determination. High-resolution structures were obtained using ARIA. Final structures are based on a total of 3966 restraints, 3523 are NOE-derived distance constraints, 443 dihedral angle restraints, 96 distance restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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