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- EMDB-35152: Structure of SFTSV virion -

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Basic information

Entry
Database: EMDB / ID: EMD-35152
TitleStructure of SFTSV virion
Map dataSFTSV full virion
Sample
  • Virus: Dabie bandavirus
    • Protein or peptide: Gn glycoprotein
    • Protein or peptide: Gc glycoprotein
KeywordsSFTSV / virion / icosahedral reconstruction / VIRUS
Biological speciesDabie bandavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsDu S / Peng R / Qi J / Li C
Funding support China, 1 items
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 17, 2023-
Header (metadata) releaseSep 13, 2023-
Map releaseSep 13, 2023-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35152.png

Downloads & links

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Map

FileDownload / File: emd_35152.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSFTSV full virion
Voxel sizeX=Y=Z: 3.36 Å
Density
Contour LevelBy AUTHOR: 5.5
Minimum - Maximum-11.619755 - 16.985613000000001
Average (Standard dev.)0.28356156 (±1.6495898)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 1209.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 2

Fileemd_35152_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_35152_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dabie bandavirus

EntireName: Dabie bandavirus
Components
  • Virus: Dabie bandavirus
    • Protein or peptide: Gn glycoprotein
    • Protein or peptide: Gc glycoprotein

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Supramolecule #1: Dabie bandavirus

SupramoleculeName: Dabie bandavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2748958 / Sci species name: Dabie bandavirus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Virus shellShell ID: 1 / Diameter: 1100.0 Å / T number (triangulation number): 12

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Macromolecule #1: Gn glycoprotein

MacromoleculeName: Gn glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Dabie bandavirus
SequenceString: MMKVIWFSSL ICLVIQCGGD SGPIICAGPI HSNKSANIPH LLGYSEKICQ IDRLIHVSSW LRNHSQFQGY VGQRGGRSQV SYYPAENSY SRWSGLLSPC DADWLGMLVV KKAKGSDMIV PGPSYKGKVF FERPTFDGYV GWGCSSGKSR TESGELCSSD S GTSSGLLP ...String:
MMKVIWFSSL ICLVIQCGGD SGPIICAGPI HSNKSANIPH LLGYSEKICQ IDRLIHVSSW LRNHSQFQGY VGQRGGRSQV SYYPAENSY SRWSGLLSPC DADWLGMLVV KKAKGSDMIV PGPSYKGKVF FERPTFDGYV GWGCSSGKSR TESGELCSSD S GTSSGLLP SDRVLWIGDV ACQPMTPIPE ETFLELKSFS QSEFPDICKI DGVVFNQCEG ESLPQPFDVA WMDVGHSHKI IM REHKTKW VQESSSKDFV CYKAGTGPCS ESEEKTCKTS GSCRGDMQFC KVAGCEHGEE ASEAKCRCSL VHKPGEVVVS YGG MRVRPK CYGFSRMMAT LEVNPPEQRT GQCTGCHLEC INGGVRLITL TSELKSATVC ASHFCSSATS GKKSTEIQFH SGSL VGRTA IHVKGALVDG TEFTFEGSCM FPDGCDAVDC TFCREFLKNP QCYPAKKWLF IIIVILLGYA GLMLLTNVLK AIGIW GSWV IAPVKLIFAI IKKLMRTVSC LMGKLMDRGR QVIHEEIGEN REGNQDDVRI EMARPRRVRH WMYSPVILTI LAIGLA

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Macromolecule #2: Gc glycoprotein

MacromoleculeName: Gc glycoprotein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Dabie bandavirus
SequenceString: ESCDEMVHAD SKLVSCRQGS GNMKECVTTG RALLPAVNPG QEACLHFTAP GSPDSKCLKI KVKRINLKCK KSSSYFVPDA RSRCTSVRR CRWAGDCQSG CPPHSTSNSF SDDWAGKMDR AGLGFSGCSD GCGGAACGCF NAAPSCIFWR KWVENPHGII W KVSPCAAW ...String:
ESCDEMVHAD SKLVSCRQGS GNMKECVTTG RALLPAVNPG QEACLHFTAP GSPDSKCLKI KVKRINLKCK KSSSYFVPDA RSRCTSVRR CRWAGDCQSG CPPHSTSNSF SDDWAGKMDR AGLGFSGCSD GCGGAACGCF NAAPSCIFWR KWVENPHGII W KVSPCAAW VPSAVIELTM PSGEVRTFHP MSGIPTQVFK GVSVTYLGSD MEVSGLTDLC EIEELKSKKL ALAPCNQAGM GV VGKVGEI QCSSEESART IKKDGCIWNA DLVGIELRVD DAVCYSKITS VEAVANYSAI PTTIGGLRFE RSHDSLGKIS GSP LDITAI RGSFSVNYRG LRLSLSEITA TCTGEVTNVS GCYSCMTGAK VSIKLHSSKN STAHVRCKGD ETAFSVLEGV HSYT VSLSF DHAVVDEQCQ LNCGGHESQV TLKGNLIFLD VPKFVDGSYM QTYHSSVPTG ANIPSPTDWL NALFGNGLSR WILGV IGVL LGGLALFFLI MSLFKLGTKQ VFRSRTKLA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

4197

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90188
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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