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Yorodumi- PDB-1qc6: EVH1 domain from ENA/VASP-like protein in complex with ACTA peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qc6 | ||||||
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Title | EVH1 domain from ENA/VASP-like protein in complex with ACTA peptide | ||||||
Components |
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Keywords | STRUCTURAL 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 / negative regulation of ruffle assembly / actin nucleation / actin filament-based movement / negative regulation of epithelial cell migration / RHO GTPases Activate Formins / profilin binding / barbed-end actin filament capping / actin polymerization or depolymerization / positive regulation of actin filament polymerization ...Signaling by ROBO receptors / negative regulation of ruffle assembly / actin nucleation / actin filament-based movement / negative regulation of epithelial cell migration / RHO GTPases Activate Formins / profilin binding / barbed-end actin filament capping / actin polymerization or depolymerization / positive regulation of actin filament polymerization / phagocytic vesicle / positive regulation of stress fiber assembly / axon guidance / platelet activation / SH3 domain binding / cellular response to type II interferon / lamellipodium / actin binding / protein homotetramerization / cytoskeleton / focal adhesion / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Fedorov, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qc6.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qc6.ent.gz | 43.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/1qc6 ftp://data.pdbj.org/pub/pdb/validation_reports/qc/1qc6 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is constructed from chains 1A and 2A / The biological assembly is constructed from chains 1B and 2B |
-Components
#1: 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 | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.980544, 0.978455, 0.941310 | ||||||||||||
Detector | Type: ADSC / Detector: CCD / Date: Feb 15, 1999 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | |||||||||||||||||||||||||
Xplor file | Serial 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
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