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- EMDB-31579: Cryo-EM structure of CCHFV envelope protein Gc in postfusion conf... -

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Basic information

Entry
Database: EMDB / ID: EMD-31579
TitleCryo-EM structure of CCHFV envelope protein Gc in postfusion conformation
Map data
Sample
  • Complex: CCHFV envelope protein Gc
    • Protein or peptide: Glycoprotein C
KeywordsCCHFV / envelope protein / postfusion / Bunyavirus / VIRAL PROTEIN
Function / homology
Function and homology information


host cell Golgi membrane / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Nairovirus M polyprotein-like / : / : / : / : / Nairovirus GP38 / Nairovirus, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Hantavirus glycoprotein Gc ...Nairovirus M polyprotein-like / : / : / : / : / Nairovirus GP38 / Nairovirus, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus strain IbAr10200
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLi N / Rao G
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570161 China
CitationJournal: Virol Sin / Year: 2022
Title: Cryo-EM structure of glycoprotein C from Crimean-Congo hemorrhagic fever virus.
Authors: Na Li / Guibo Rao / Zhiqiang Li / Jiayi Yin / Tingting Chong / Kexing Tian / Yan Fu / Sheng Cao /
Abstract: Crimean-Congo hemorrhagic fever virus (CCHFV) is a causative agent of serious hemorrhagic diseases in humans with high mortality rates. CCHFV glycoprotein Gc plays critical roles in mediating virus- ...Crimean-Congo hemorrhagic fever virus (CCHFV) is a causative agent of serious hemorrhagic diseases in humans with high mortality rates. CCHFV glycoprotein Gc plays critical roles in mediating virus-host membrane fusion and has been studied extensively as an immunogen. However, the molecular mechanisms involved in membrane fusion and Gc-specific antibody-antigen interactions remain unresolved largely because structural information of this glycoprotein is missing. We designed a trimeric protein including most of the ectodomain region of Gc from the prototype CCHFV strain, IbAr10200, which enabled the cryo-electron microscopy structure to be solved at a resolution of 2.8 ​Å. The structure confirms that CCHFV Gc is a class II fusion protein. Unexpectedly, structural comparisons with other solved Gc trimers in the postfusion conformation revealed that CCHFV Gc adopted hybrid architectural features of the fusion loops from hantaviruses and domain III from phenuiviruses, suggesting a complex evolutionary pathway among these bunyaviruses. Antigenic sites on CCHFV Gc that protective neutralizing antibodies target were mapped onto the CCHFV Gc structure, providing valuable information that improved our understanding of potential neutralization mechanisms of various antibodies.
History
DepositionJul 26, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.44
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.44
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7fgf
  • Surface level: 0.44
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31579.png

Downloads & links

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Map

FileDownload / File: emd_31579.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.61 Å/pix.
x 360 pix.
= 219.6 Å		0.61 Å/pix.
x 360 pix.
= 219.6 Å		0.61 Å/pix.
x 360 pix.
= 219.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.61 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.44 / Movie #1: 0.44
Minimum - Maximum-2.404114 - 3.4646294
Average (Standard dev.)-0.0020319964 (±0.09588593)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 219.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.610.610.61
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z219.600219.600219.600
α/β/γ90.00090.00090.000
start NX/NY/NZ139118109
NX/NY/NZ123164187
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-2.4043.465-0.002

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Supplemental data

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Sample components

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Entire : CCHFV envelope protein Gc

EntireName: CCHFV envelope protein Gc
Components
  • Complex: CCHFV envelope protein Gc
    • Protein or peptide: Glycoprotein C

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Supramolecule #1: CCHFV envelope protein Gc

SupramoleculeName: CCHFV envelope protein Gc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Crimean-Congo hemorrhagic fever virus strain IbAr10200

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Macromolecule #1: Glycoprotein C

MacromoleculeName: Glycoprotein C / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Crimean-Congo hemorrhagic fever virus strain IbAr10200
Strain: IbAr10200
Molecular weightTheoretical: 65.809711 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: MKNLLNSTSL ETSLSIEAPW GAINVQSTYK PTVSTANIAL SWSSVEHRGN KILVSGRSES IMKLEERTGI SWDLGVEDAS ESKLLTVSV MDLSQMYSPV FEYLSGDRQV GEWPKATCTG DCPERCGCTS STCLHKEWPH SRNWRCNPTW CWGVGTGCTC C GLDVKDLF ...String:
MKNLLNSTSL ETSLSIEAPW GAINVQSTYK PTVSTANIAL SWSSVEHRGN KILVSGRSES IMKLEERTGI SWDLGVEDAS ESKLLTVSV MDLSQMYSPV FEYLSGDRQV GEWPKATCTG DCPERCGCTS STCLHKEWPH SRNWRCNPTW CWGVGTGCTC C GLDVKDLF TDYMFVKWKV EYIKTEAIVC VELTSQERQC SLIEAGTRFN LGPVTITLSE PRNIQQKLPP EIITLHPRIE EG FFDLMHV QKVLSASTVC KLQSCTHGVP GDLQVYHIGN LLKGDKVNGH LIHKIEPHFN TSWMSWDGCD LDYYCNMGDW PSC TYTGVT QHNHASFVNL LNIETDYTKN FHFHSKRVTA HGDTPQLDLK ARPTYGAGEI TVLVEVADME LHTKKIEISG LKFA SLACT GCYACSSGIS CKVRIHVDEP DELTVHVKSD DPDVVAASSS LMARKLEFGT DSTFKAFSAM PKTSLCFYIV EREHC KSCS EEDTKKCVNT KLEQPQSILI EHKGTIIGKQ NSTCTAKSRG SGGMKQIEDK IEEILSKIYH IENEIARIKK LIGEGS GGS RGPFEGKPIP NPLLGLDSTR TGHHHHHH

UniProtKB: Envelopment polyprotein

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 187292
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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