+Open data
-Basic information
Entry | Database: PDB / ID: 5h9c | ||||||
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Title | Crystal structure of the ASLV fusion protein core | ||||||
Components | Envelope glycoprotein gp95 | ||||||
Keywords | VIRAL PROTEIN / fusion / ASLV / glycoprotein / entry / virus | ||||||
Function / homology | Function and homology information symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Avian leukosis virus RSA | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.783 Å | ||||||
Authors | Aydin, H. / Lee, J.E. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Faseb J. / Year: 2013 Title: Structural characterization of a fusion glycoprotein from a retrovirus that undergoes a hybrid 2-step entry mechanism. Authors: Aydin, H. / Smrke, B.M. / Lee, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h9c.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h9c.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 5h9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/5h9c ftp://data.pdbj.org/pub/pdb/validation_reports/h9/5h9c | HTTPS FTP |
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-Related structure data
Related structure data | 4jprSC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 10579.786 Da / Num. of mol.: 1 / Mutation: C499S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Avian leukosis virus RSA / Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: P03397 |
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#2: Chemical | ChemComp-CL / |
#3: 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: 1.99 Å3/Da / Density % sol: 38.18 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% (w/v) 2-methyl-2,4-pentanediol, 5% (w/v) PEG 8000, and 0.1 M sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→39.81 Å / Num. obs: 7712 / % possible obs: 98.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.38 |
Reflection shell | Resolution: 1.78→1.82 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 1.7 / % possible all: 80.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JPR Resolution: 1.783→39.809 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.783→39.809 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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