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- PDB-6h3u: Schmallenberg Virus Glycoprotein Gc Head Domain in Complex with s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6h3u | |||||||||
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Title | Schmallenberg Virus Glycoprotein Gc Head Domain in Complex with scFv 4B6 | |||||||||
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![]() | VIRAL PROTEIN / Envelope Glycoprotein / scFv Antibody | |||||||||
Function / homology | ![]() modulation by virus of host process / host cell Golgi membrane / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | 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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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 413.4 KB | Display | ![]() |
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PDB format | ![]() | 343.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 36.5 KB | Display | |
Data in CIF | ![]() | 49.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6h3sC ![]() 6h3tSC ![]() 6h3vC ![]() 6h3wC ![]() 6h3xC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 15066.347 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 12906.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 28379.520 Da / Num. of mol.: 2 / Fragment: Glycoprotein Gc Head Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.31 Å3/Da / Density % sol: 80.51 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.75 uL of a 22.8 mg/mL solution of the GPC-purified complex in 20 mM Tris-Cl pH 8.0, 150 mM NaCl were added to 0.75 uL of reservoir solution containing 0.1 M sodium acetate pH 4.6, 3.5 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980097 Å / Relative weight: 1 |
Reflection | Resolution: 3.168→48.554 Å / Num. obs: 27774 / % possible obs: 59.1 % / Observed criterion σ(I): 1.2 / Redundancy: 20.9 % / CC1/2: 1 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.05 / Rrim(I) all: 0.23 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 3.17→3.61 Å / Redundancy: 18.7 % / Rmerge(I) obs: 1.78 / Mean I/σ(I) obs: 2 / Num. unique obs: 1391 / CC1/2: 0.72 / Rpim(I) all: 0.41 / Rrim(I) all: 1.82 / % possible all: 9.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6H3T along with a Phyre2-generated model of the scFv 4B6 antibody fragment Resolution: 3.168→48.554 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 240.86 Å2 / Biso mean: 113.1078 Å2 / Biso min: 47.16 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.168→48.554 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: 14
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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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