[English] 日本語
Yorodumi
- EMDB-35183: Structure of the asymmetric unit of SFTSV virion -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35183
TitleStructure of the asymmetric unit of SFTSV virion
Map datacomposite map of the asymmetric unit of SFTSV virion
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: 5.2 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 21, 2023-
Header (metadata) releaseSep 13, 2023-
Map releaseSep 13, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35183.png

Downloads & links

-
Map

FileDownload / File: emd_35183.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map of the asymmetric unit of SFTSV virion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.68 Å/pix.
x 300 pix.
= 504. Å		1.68 Å/pix.
x 300 pix.
= 504. Å		1.68 Å/pix.
x 300 pix.
= 504. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.1
Minimum - Maximum-5.531002 - 15.161467999999999
Average (Standard dev.)0.038789254 (±0.43660927)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 503.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: subtomogram averaging density map of SFTSV virion hexon peplomer

Fileemd_35183_additional_1.map
Annotationsubtomogram averaging density map of SFTSV virion hexon peplomer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
Supramolecule #1: Dabie bandavirus

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

-
Macromolecule #1: Envelopment polyprotein

MacromoleculeName: Envelopment polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / 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

-
Macromolecule #2: Envelopment polyprotein

MacromoleculeName: Envelopment polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / 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

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 54 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

4197

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: OTHER / Details: Model vs map FSC 0.5 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)

-
Atomic model buiding 1

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

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more