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- EMDB-35540: Structure of SFTSV Gn-Gc heterodimer -

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Basic information

Entry
Database: EMDB / ID: EMD-35540
TitleStructure of SFTSV Gn-Gc heterodimer
Map datalocally averaged map of SFTSV Gn-Gc heterodimer
Sample
  • Virus: Dabie bandavirus
    • Protein or peptide: Envelopment polyprotein
    • Protein or peptide: Envelopment polyprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSFTSV / virion / icosahedral reconstruction / VIRUS / VIRAL PROTEIN
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 / Dabie bandavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 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
DepositionMar 4, 2023-
Header (metadata) releaseSep 13, 2023-
Map releaseSep 13, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35540.png

Downloads & links

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Map

FileDownload / File: emd_35540.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocally averaged map of SFTSV Gn-Gc heterodimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.7
Minimum - Maximum-49.812759999999997 - 66.442276000000007
Average (Standard dev.)0.000000000012557 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 215.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Dabie bandavirus

EntireName: Dabie bandavirus
Components
  • Virus: Dabie bandavirus
    • Protein or peptide: Envelopment polyprotein
    • Protein or peptide: Envelopment polyprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Dabie bandavirus

SupramoleculeName: Dabie bandavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 1003835 / 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: Envelopment polyprotein

MacromoleculeName: Envelopment polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe fever with thrombocytopenia syndrome virus
Molecular weightTheoretical: 61.751246 KDa
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

UniProtKB: Envelopment polyprotein

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Macromolecule #2: Envelopment polyprotein

MacromoleculeName: Envelopment polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe fever with thrombocytopenia syndrome virus
Molecular weightTheoretical: 54.994797 KDa
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

UniProtKB: Envelopment polyprotein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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 / 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: 300 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: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: OTHER / Details: model vs map FSC 0.5 cut-off / Number images used: 2249030
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient
Output model

PDB-8ilq:
Structure of SFTSV Gn-Gc heterodimer

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