+Open data
-Basic information
Entry | Database: PDB / ID: 6h3w | |||||||||
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Title | La Crosse Virus Glycoprotein Gc Head Domain | |||||||||
Components | Envelopment polyprotein | |||||||||
Keywords | VIRAL PROTEIN / Envelope Glycoprotein | |||||||||
Function / homology | Function and homology information modulation by virus of host process / host cell Golgi membrane / host cell endoplasmic reticulum membrane / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | Bunyavirus La Crosse | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å | |||||||||
Authors | Hellert, J. / Aebischer, A. / Wernike, K. / Haouz, A. / Brocchi, E. / Reiche, S. / Guardado-Calvo, P. / Beer, M. / Rey, F.A. | |||||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Orthobunyavirus spike architecture and recognition by neutralizing antibodies. Authors: Hellert, J. / Aebischer, A. / Wernike, K. / Haouz, A. / Brocchi, E. / Reiche, S. / Guardado-Calvo, P. / Beer, M. / 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 | 6h3w.cif.gz | 121.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h3w.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 6h3w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h3w_validation.pdf.gz | 795.1 KB | Display | wwPDB validaton report |
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Full document | 6h3w_full_validation.pdf.gz | 796.7 KB | Display | |
Data in XML | 6h3w_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 6h3w_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/6h3w ftp://data.pdbj.org/pub/pdb/validation_reports/h3/6h3w | HTTPS FTP |
-Related structure data
Related structure data | 6h3sC 6h3tC 6h3uC 6h3vC 6h3xSC 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: 28576.375 Da / Num. of mol.: 1 / Fragment: Glycoprotein Gc Head Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bunyavirus La Crosse / Gene: GP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8JPR1 |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-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: 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: 2.57 Å3/Da / Density % sol: 52.16 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.75 uL of a 11.1 mg/mL protein sample in 20 mM Tris-Cl pH 8.0, 150 mM NaCl were added to 0.75 uL of reservoir solution containing 0.1 M HEPES pH7.5, 10% v/v 2-propanol, 20% w/v PEG 4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97717 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97717 Å / Relative weight: 1 |
Reflection | Resolution: 2.098→47.052 Å / Num. obs: 17376 / % possible obs: 99.3 % / Redundancy: 7.9 % / Biso Wilson estimate: 44.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1378 / CC1/2: 0.65 / Rpim(I) all: 0.39 / Rrim(I) all: 1.09 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6H3X Resolution: 2.098→47.052 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 19.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.62 Å2 / Biso mean: 31.7246 Å2 / Biso min: 7.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.098→47.052 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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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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