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Open data
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Basic information
Entry | Database: PDB / ID: 8xk8 | ||||||
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Title | N1D10 Fab bound to SFTSV glycoprotein-Gn | ||||||
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![]() | VIRAL PROTEIN / glycoprotein / Gn / Fab | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhao, H. / Deng, Z. | ||||||
Funding support | 1items
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![]() | ![]() Title: A broadly protective antibody targeting the 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. / Yang, S. / Hu, Y. / Deng, Z. / Ning, Y. / Zhao, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 553.2 KB | Display | ![]() |
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PDB format | ![]() | 454.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.8 KB | Display | ![]() |
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Full document | ![]() | 510.5 KB | Display | |
Data in XML | ![]() | 53.3 KB | Display | |
Data in CIF | ![]() | 73 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8xk5C ![]() 8xk6C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39523.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() #2: Antibody | Mass: 26368.611 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | Mass: 26020.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.17 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.095 M tri-Sodium citrate pH 5.6, 19 %(v/v) Isopropanol, 19 %(w/v) PEG 4000, 5 %(v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 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: 3.52→47.16 Å / Num. obs: 20028 / % possible obs: 98.5 % / Redundancy: 2.7 % / CC1/2: 0.758 / Net I/σ(I): 3.4 |
Reflection shell | Resolution: 3.52→3.85 Å / Redundancy: 2.6 % / Num. unique obs: 4658 / CC1/2: 0.626 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 3.53→20.69 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: 36.627 Å / Origin y: -24.1179 Å / Origin z: 22.921 Å
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Refinement TLS group | Selection details: all |