+Open data
-Basic information
Entry | Database: PDB / ID: 8ilq | ||||||
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Title | Structure of SFTSV Gn-Gc heterodimer | ||||||
Components | (Envelopment polyprotein) x 2 | ||||||
Keywords | VIRAL PROTEIN / SFTSV / virion / icosahedral reconstruction / VIRUS | ||||||
Function / homology | Function and homology information 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 | Severe fever with thrombocytopenia syndrome virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
Authors | Du, S. / Peng, R. / Qi, J. / Li, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM structure of severe fever with thrombocytopenia syndrome virus. Authors: Shouwen Du / Ruchao Peng / Wang Xu / Xiaoyun Qu / Yuhang Wang / Jiamin Wang / Letian Li / Mingyao Tian / Yudong Guan / Jigang Wang / Guoqing Wang / Hao Li / Lingcong Deng / Xiaoshuang Shi / ...Authors: Shouwen Du / Ruchao Peng / Wang Xu / Xiaoyun Qu / Yuhang Wang / Jiamin Wang / Letian Li / Mingyao Tian / Yudong Guan / Jigang Wang / Guoqing Wang / Hao Li / Lingcong Deng / Xiaoshuang Shi / Yidan Ma / Fengting Liu / Minhua Sun / Zhengkai Wei / Ningyi Jin / Wei Liu / Jianxun Qi / Quan Liu / Ming Liao / Chang Li / Abstract: The severe fever with thrombocytopenia syndrome virus (SFTSV) is a tick-borne human-infecting bunyavirus, which utilizes two envelope glycoproteins, Gn and Gc, to enter host cells. However, the ...The severe fever with thrombocytopenia syndrome virus (SFTSV) is a tick-borne human-infecting bunyavirus, which utilizes two envelope glycoproteins, Gn and Gc, to enter host cells. However, the structure and organization of these glycoproteins on virion surface are not yet known. Here we describe the structure of SFTSV determined by single particle reconstruction, which allows mechanistic insights into bunyavirus assembly at near-atomic resolution. The SFTSV Gn and Gc proteins exist as heterodimers and further assemble into pentameric and hexameric peplomers, shielding the Gc fusion loops by both intra- and inter-heterodimer interactions. Individual peplomers are associated mainly through the ectodomains, in which the highly conserved glycans on N914 of Gc play a crucial role. This elaborate assembly stabilizes Gc in the metastable prefusion conformation and creates some cryptic epitopes that are only accessible in the intermediate states during virus entry. These findings provide an important basis for developing vaccines and therapeutic drugs. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ilq.cif.gz | 187.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ilq.ent.gz | 144.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ilq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ilq_validation.pdf.gz | 786.8 KB | Display | wwPDB validaton report |
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Full document | 8ilq_full_validation.pdf.gz | 799.4 KB | Display | |
Data in XML | 8ilq_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 8ilq_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/8ilq ftp://data.pdbj.org/pub/pdb/validation_reports/il/8ilq | HTTPS FTP |
-Related structure data
Related structure data | 35540MC 8i4tC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 61751.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Severe fever with thrombocytopenia syndrome virus References: UniProt: A0A4D6J0G9 | ||
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#2: Protein | Mass: 54994.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Severe fever with thrombocytopenia syndrome virus References: UniProt: A0A4D6J0G9 | ||
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Sugar | ChemComp-NAG / Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Dabie bandavirus / Type: VIRUS / Entity ID: #1-#2 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Dabie bandavirus |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Virus shell | Diameter: 1100 nm / Triangulation number (T number): 12 |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: OTHER / Num. of particles: 2249030 / Algorithm: FOURIER SPACE / Details: model vs map FSC 0.5 cut-off / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||
Refine LS restraints |
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