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Yorodumi- PDB-4ojc: Crystal structure of the wild-type full-length trimeric ectodomai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ojc | |||||||||
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Title | Crystal structure of the wild-type full-length trimeric ectodomain of the C. elegans fusion protein EFF-1 | |||||||||
Components | EFF-1A | |||||||||
Keywords | MEMBRANE PROTEIN / class II fusion protein / membrane fusion protein / cell surface | |||||||||
Function / homology | Function and homology information nematode male tail mating organ morphogenesis / fusogenic activity / EFF-1 complex / chordate pharyngeal muscle development / post-embryonic body morphogenesis / nematode male tail tip morphogenesis / vulval development / cell-cell fusion / syncytium formation by plasma membrane fusion / embryonic body morphogenesis ...nematode male tail mating organ morphogenesis / fusogenic activity / EFF-1 complex / chordate pharyngeal muscle development / post-embryonic body morphogenesis / nematode male tail tip morphogenesis / vulval development / cell-cell fusion / syncytium formation by plasma membrane fusion / embryonic body morphogenesis / egg-laying behavior / cell-cell contact zone / locomotion / morphogenesis of an epithelium / kinase activity / phosphorylation / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Caenorhabditis elegans (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.93 Å | |||||||||
Authors | Krey, T. / Rey, F.A. | |||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2014 Title: Structural basis of eukaryotic cell-cell fusion Authors: Perez-Vargas, J. / Krey, T. / Valansi, C. / Avinoam, O. / Haouz, A. / Jamin, M. / Raveh-Barak, H. / Podbilewicz, B. / Rey, F.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ojc.cif.gz | 107.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ojc.ent.gz | 83.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ojc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/4ojc ftp://data.pdbj.org/pub/pdb/validation_reports/oj/4ojc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 64947.637 Da / Num. of mol.: 1 / Fragment: UNP residues 23-561 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: C26D10.5, CELE_C26D10.5, eff-1 / Plasmid: pMT-based / Cell (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: G5ECA1 | ||||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Sugar | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2% 2-Propanol, 50mM sodium citrate, 0.8-1.2M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0396 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2010 |
Radiation | Monochromator: LN2 cooled Fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0396 Å / Relative weight: 1 |
Reflection | Resolution: 2.93→50 Å / Num. all: 18909 / Num. obs: 18417 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 113.4 Å2 |
Reflection shell | Resolution: 2.93→3.09 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 2735 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.93→46.42 Å / Cor.coef. Fo:Fc: 0.9231 / Cor.coef. Fo:Fc free: 0.8869 / SU R Cruickshank DPI: 0.814 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 92.38 Å2
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Refine analyze | Luzzati coordinate error obs: 0.549 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.93→46.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.93→3.11 Å / Total num. of bins used: 9
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