+Open data
-Basic information
Entry | Database: PDB / ID: 8xk5 | ||||||
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Title | SNB1G11 Fab bound to SFTSV glycoprotein Gn | ||||||
Components |
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Keywords | VIRAL PROTEIN / glycoprotein / Gn / Fab | ||||||
Function / homology | Function and homology information host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Severe fever with thrombocytopenia syndrome virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | ||||||
Authors | Deng, Z. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: A broadly protective antibody targeting glycoprotein Gn inhibits severe fever with thrombocytopenia syndrome virus infection. Authors: Ren, X. / Sun, J. / Kuang, W. / Yu, F. / Wang, B. / Wang, Y. / Deng, W. / Xu, Z. / Yang, S. / Wang, H. / Hu, Y. / Deng, Z. / Ning, Y.J. / Zhao, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xk5.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8xk5.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 8xk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xk5_validation.pdf.gz | 594.4 KB | Display | wwPDB validaton report |
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Full document | 8xk5_full_validation.pdf.gz | 704.9 KB | Display | |
Data in XML | 8xk5_validation.xml.gz | 127.2 KB | Display | |
Data in CIF | 8xk5_validation.cif.gz | 173 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/8xk5 ftp://data.pdbj.org/pub/pdb/validation_reports/xk/8xk5 | HTTPS FTP |
-Related structure data
Related structure data | 8xk6C 8xk8C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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5 |
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Unit cell |
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-Components
#1: Antibody | Mass: 27999.414 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fab heavy chain / Production host: Homo sapiens (human) #2: Antibody | Mass: 25380.344 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fab light chain / Production host: Homo sapiens (human) #3: Protein | Mass: 39523.969 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe fever with thrombocytopenia syndrome virus Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R4V2Q5 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.91 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 20 % (w/v) Jeffamine ED2003, 0.1M HEPES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 27, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→30 Å / Num. obs: 79582 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.997 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 3.05→3.1 Å / Redundancy: 5.1 % / Num. unique obs: 5119 / CC1/2: 0.543 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→29.97 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→29.97 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -51.3935 Å / Origin y: 2.4523 Å / Origin z: -33.5303 Å
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Refinement TLS group | Selection details: all |