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- PDB-8i4t: Structure of the asymmetric unit of SFTSV virion -

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Basic information

Entry
Database: PDB / ID: 8i4t
TitleStructure of the asymmetric unit of SFTSV virion
Components(Envelopment polyprotein) x 2
KeywordsVIRAL 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
Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesSevere fever with thrombocytopenia syndrome virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsDu, S. / Peng, R. / Qi, J. / Li, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31972719 China
CitationJournal: 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
DepositionJan 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Envelopment polyprotein
F: Envelopment polyprotein
A: Envelopment polyprotein
B: Envelopment polyprotein
C: Envelopment polyprotein
H: Envelopment polyprotein
D: Envelopment polyprotein
I: Envelopment polyprotein
E: Envelopment polyprotein
J: Envelopment polyprotein
U: Envelopment polyprotein
K: Envelopment polyprotein
X: Envelopment polyprotein
L: Envelopment polyprotein
T: Envelopment polyprotein
M: Envelopment polyprotein
O: Envelopment polyprotein
Q: Envelopment polyprotein
V: Envelopment polyprotein
R: Envelopment polyprotein
N: Envelopment polyprotein
P: Envelopment polyprotein
S: Envelopment polyprotein
W: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,415,44484
Polymers1,400,95324
Non-polymers14,49260
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, homology
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Envelopment polyprotein / Gc / M polyprotein


Mass: 54994.797 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Severe fever with thrombocytopenia syndrome virus
References: UniProt: A0A4D6J0G9
#2: Protein
Envelopment polyprotein / Gn / M polyprotein


Mass: 61751.246 Da / Num. of mol.: 12 / 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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dabie bandavirus / Type: VIRUS / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Dabie bandavirus
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Virus shellDiameter: 1100 nm / Triangulation number (T number): 12
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
4Gctf1.06CTF correction
7UCSF Chimera1.13model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
13PHENIX1.17model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.2 Å / Resolution method: OTHER / Num. of particles: 90188 / Algorithm: FOURIER SPACE / Details: Model vs map FSC 0.5 cut-off / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient

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