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- PDB-1egx: SOLUTION STRUCTURE OF THE ENA-VASP HOMOLOGY 1 (EVH1) DOMAIN OF HU... -

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Basic information

Entry
Database: PDB / ID: 1egx
TitleSOLUTION STRUCTURE OF THE ENA-VASP HOMOLOGY 1 (EVH1) DOMAIN OF HUMAN VASODILATOR-STIMULATED PHOSPHOPROTEIN (VASP)
ComponentsVASODILATOR-STIMULATED PHOSPHOPROTEIN
KeywordsSIGNALING PROTEIN / EVH1 / VASP-Ena / POLY-PROLINE-BINDING DOMAIN
Function / homology
Function and homology information


profilin binding / Signaling by ROBO receptors / Cell-extracellular matrix interactions / actin polymerization or depolymerization / filopodium membrane / positive regulation of actin filament polymerization / lamellipodium membrane / Generation of second messenger molecules / bicellular tight junction / neural tube closure ...profilin binding / Signaling by ROBO receptors / Cell-extracellular matrix interactions / actin polymerization or depolymerization / filopodium membrane / positive regulation of actin filament polymerization / lamellipodium membrane / Generation of second messenger molecules / bicellular tight junction / neural tube closure / axon guidance / SH3 domain binding / actin cytoskeleton / actin binding / actin cytoskeleton organization / protein homotetramerization / cadherin binding / focal adhesion / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Vasodilator-stimulated phosphoprotein/ENA/VASP-like / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like ...Vasodilator-stimulated phosphoprotein/ENA/VASP-like / VASP tetramerisation / VASP tetramerisation domain superfamily / VASP tetramerisation domain / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Vasodilator-stimulated phosphoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics
AuthorsBall, L. / Kuhne, R. / Hoffmann, B. / Hafner, A. / Schmieder, P. / Volkmer-Engert, R. / Hof, M. / Wahl, M. / Schneider-Mergener, J. / Walter, U. ...Ball, L. / Kuhne, R. / Hoffmann, B. / Hafner, A. / Schmieder, P. / Volkmer-Engert, R. / Hof, M. / Wahl, M. / Schneider-Mergener, J. / Walter, U. / Oschkinat, H. / Jarchau, T.
CitationJournal: EMBO J. / Year: 2000
Title: Dual epitope recognition by the VASP EVH1 domain modulates polyproline ligand specificity and binding affinity.
Authors: Ball, L.J. / Kuhne, R. / Hoffmann, B. / Hafner, A. / Schmieder, P. / Volkmer-Engert, R. / Hof, M. / Wahl, M. / Schneider-Mergener, J. / Walter, U. / Oschkinat, H. / Jarchau, T.
History
DepositionFeb 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 25, 2012Group: Other
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VASODILATOR-STIMULATED PHOSPHOPROTEIN


Theoretical massNumber of molelcules
Total (without water)12,7461
Polymers12,7461
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)15 / 200structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1fewest violations, lowest energy

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Components

#1: Protein VASODILATOR-STIMULATED PHOSPHOPROTEIN / VASP


Mass: 12746.359 Da / Num. of mol.: 1 / Fragment: EVH1 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P50552

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1312D NOESY
141DQF-COSY
151HNHA
1613D (H)CCH-TOCSY
1713D HNHB
1813D CBCA(CO)NNH
1913D CBCANNH
11013D 15N-separated-TOCSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 1.3 mM VASP EVH1 DOMAIN 15N,13C; buffer containing 20 mM KH2PO4, 50 mM KCl, 0.2 mM Na3N3; samples were used in both 90% H2O,10% D2O and 99.8% D2O 2 mM VASP EVH1 DOMAIN 15N buffer containing ...Contents: 1.3 mM VASP EVH1 DOMAIN 15N,13C; buffer containing 20 mM KH2PO4, 50 mM KCl, 0.2 mM Na3N3; samples were used in both 90% H2O,10% D2O and 99.8% D2O 2 mM VASP EVH1 DOMAIN 15N buffer containing 20 mM KH2PO4, 50 mM KCl, 0.2 mM Na3N3;sample were used in 90% H2O,10% D2O
Solvent system: 90% H2O,10% D2O and 99.8% D2O
Sample conditionsIonic strength: 50 mM KCl, 20 mM KH2PO4 / pH: 6.0 / Pressure: 1 atm / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
CNS09aBrungerstructure solution
Azara2.1Boucherprocessing
XwinNMR1.3Brukerprocessing
ANSIG3.3Krauliscollection
CNS09aBrungerrefinement
RefinementMethod: simulated annealing torsion angle dynamics / Software ordinal: 1
Details: structures are based on 3043 NOE-derived distance restraints, 49 dihedral angle restraints, 25 distance restraints from hydrogen bonds
NMR representativeSelection criteria: fewest violations, lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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