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- PDB-1qc6: EVH1 domain from ENA/VASP-like protein in complex with ACTA peptide -

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Basic information

Entry
Database: PDB / ID: 1qc6
TitleEVH1 domain from ENA/VASP-like protein in complex with ACTA peptide
Components
  • EVH1 DOMAIN FROM ENA/VASP-LIKE PROTEIN
  • PHE-GLU-PHE-PRO-PRO-PRO-PRO-THR-ASP-GLU-GLU
KeywordsSTRUCTURAL PROTEIN / AN INCOMPLETE SEVEN STRANDED ANTI-PARALLEL BETA BARREL CLOSED BY AN ALPHA HELIX / EVH1 DOMAIN / ACTIN-BASED CELL MOTILITY / INTERACTION MODULE
Function / homology
Function and homology information


Signaling by ROBO receptors / actin nucleation / RHO GTPases Activate Formins / profilin binding / actin filament-based movement / barbed-end actin filament capping / actin polymerization or depolymerization / positive regulation of actin filament polymerization / stress fiber / phagocytic vesicle ...Signaling by ROBO receptors / actin nucleation / RHO GTPases Activate Formins / profilin binding / actin filament-based movement / barbed-end actin filament capping / actin polymerization or depolymerization / positive regulation of actin filament polymerization / stress fiber / phagocytic vesicle / axon guidance / platelet activation / cellular response to type II interferon / SH3 domain binding / lamellipodium / actin binding / protein homotetramerization / focal adhesion / cytoplasm
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
Ena/VASP-like protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Gertler, F.B. / Almo, S.C.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Structure of EVH1, a novel proline-rich ligand-binding module involved in cytoskeletal dynamics and neural function
Authors: Fedorov, A.A. / Fedorov, E. / Gertler, F. / Almo, S.C.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Mena, a relative of VASP and Drosophila Enabled is implicated in the control of microfilament dynamics
Authors: Gertler, F.B. / Niebuhr, K. / Reinhard, M. / Wehland, J. / Soriano, P.
History
DepositionMay 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _exptl_crystal_grow.temp_details
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EVH1 DOMAIN FROM ENA/VASP-LIKE PROTEIN
C: PHE-GLU-PHE-PRO-PRO-PRO-PRO-THR-ASP-GLU-GLU
B: EVH1 DOMAIN FROM ENA/VASP-LIKE PROTEIN
D: PHE-GLU-PHE-PRO-PRO-PRO-PRO-THR-ASP-GLU-GLU


Theoretical massNumber of molelcules
Total (without water)32,2034
Polymers32,2034
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.883, 68.257, 82.219
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThe biological assembly is constructed from chains 1A and 2A / The biological assembly is constructed from chains 1B and 2B

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Components

#1: Protein EVH1 DOMAIN FROM ENA/VASP-LIKE PROTEIN


Mass: 14796.967 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN / Mutation: MET 1,14,105,112 MODIFIED TO SELENOMET
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: brain / Plasmid: GST-FUSION / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P70429
#2: Protein/peptide PHE-GLU-PHE-PRO-PRO-PRO-PRO-THR-ASP-GLU-GLU


Mass: 1304.355 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THE PROLINE-RICH PEPTIDE PREPARED BY PEPTIDE SYNTHESIS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, DTT, sodium azide, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Temp details: room temperature
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-14 mg/mlprotein1drop
21.7 Mammonium sulfate1reservoir
35 mMdithiothreitol1reservoir
40.02 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.980544, 0.978455, 0.941310
DetectorType: ADSC / Detector: CCD / Date: Feb 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9805441
20.9784551
30.941311
ReflectionResolution: 2.6→20 Å / Num. all: 8216 / Num. obs: 7926 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 4.8 / Num. unique all: 723 / % possible all: 88.1
Reflection
*PLUS
Rmerge(I) obs: 0.09

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
DMmodel building
X-PLOR3.851refinement
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→8 Å / Rfactor Rfree error details: random / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 610 8 %random
Rwork0.215 ---
all0.237 7926 --
obs0.225 7290 92.5 %-
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 0 7 1849
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.34
X-RAY DIFFRACTIONx_dihedral_angle_d28.91
X-RAY DIFFRACTIONx_improper_angle_d0.707
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.91
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.707

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