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Yorodumi- PDB-3duz: Crystal structure of the postfusion form of baculovirus fusion pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3duz | ||||||
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Title | Crystal structure of the postfusion form of baculovirus fusion protein GP64 | ||||||
Components | Major envelope glycoprotein | ||||||
Keywords | VIRAL PROTEIN / Fusion protein / coiled-coil / fusion peptide / trimer / viral / Glycoprotein / Lipoprotein / Membrane / Palmitate / Phosphoprotein / Transmembrane / Virion | ||||||
Function / homology | Function and homology information modulation by virus of host process / membrane fusion involved in viral entry into host cell / viral budding from plasma membrane / membrane => GO:0016020 / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Autographa californica nuclear polyhedrosis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.95 Å | ||||||
Authors | Kadlec, J. / Loureiro, S. / Abrescia, N.G.A. / Jones, I.M. / Stuart, D.I. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: The postfusion structure of baculovirus gp64 supports a unified view of viral fusion machines. Authors: Kadlec, J. / Loureiro, S. / Abrescia, N.G. / Stuart, D.I. / Jones, I.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3duz.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3duz.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 3duz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/3duz ftp://data.pdbj.org/pub/pdb/validation_reports/du/3duz | 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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-Components
#1: Protein | Mass: 55872.758 Da / Num. of mol.: 1 / Fragment: UNP residues 21-499 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Autographa californica nuclear polyhedrosis virus Gene: GP67, P67 / Plasmid: BacPAK6 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P17501 |
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#2: Chemical | ChemComp-HG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 10% PEG 6000, 100 mM citric acid, 200 mM potassium sodium tartrate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0039, 0.8856, 1.0714, 1.0711 | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2007 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.95→50 Å / Num. obs: 13594 / % possible obs: 97.3 % / Observed criterion σ(I): 3.3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.3 | |||||||||||||||
Reflection shell | Resolution: 2.95→3.05 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.29 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.95→47.84 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.846 / SU B: 15.969 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.153 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→47.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.026 Å / Total num. of bins used: 20
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