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- EMDB-36407: CCHFV envelope protein Gc in complex with Gc13 -

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Basic information

Entry
Database: EMDB / ID: EMD-36407
TitleCCHFV envelope protein Gc in complex with Gc13
Map data
Sample
  • Complex: CCHFV envelope protein Gc-Gc13 complex
    • Protein or peptide: Glycoprotein C,CCHFV Gc fusion loops
    • Protein or peptide: Mouse antibody Gc13 heavy chain
    • Protein or peptide: Mouse antibody Gc13 light chain
KeywordsCCHFV / glycoprotein C / antibody / 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 / 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 / Crimean-Congo hemorrhagic fever orthonairovirus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsChong T / Cao S
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303300 China
CitationJournal: PLoS Pathog / Year: 2024
Title: Neutralizing monoclonal antibodies against the Gc fusion loop region of Crimean-Congo hemorrhagic fever virus.
Authors: Liushuai Li / Tingting Chong / Lu Peng / Yajie Liu / Guibo Rao / Yan Fu / Yanni Shu / Jiamei Shen / Qinghong Xiao / Jia Liu / Jiang Li / Fei Deng / Bing Yan / Zhihong Hu / Sheng Cao / Manli Wang /
Abstract: Crimean-Congo hemorrhagic fever virus (CCHFV) is a highly pathogenic tick-borne virus, prevalent in more than 30 countries worldwide. Human infection by this virus leads to severe illness, with an ...Crimean-Congo hemorrhagic fever virus (CCHFV) is a highly pathogenic tick-borne virus, prevalent in more than 30 countries worldwide. Human infection by this virus leads to severe illness, with an average case fatality of 40%. There is currently no approved vaccine or drug to treat the disease. Neutralizing antibodies are a promising approach to treat virus infectious diseases. This study generated 37 mouse-derived specific monoclonal antibodies against CCHFV Gc subunit. Neutralization assays using pseudotyped virus and authentic CCHFV identified Gc8, Gc13, and Gc35 as neutralizing antibodies. Among them, Gc13 had the highest neutralizing activity and binding affinity with CCHFV Gc. Consistently, Gc13, but not Gc8 or Gc35, showed in vivo protective efficacy (62.5% survival rate) against CCHFV infection in a lethal mouse infection model. Further characterization studies suggested that Gc8 and Gc13 may recognize a similar, linear epitope in domain II of CCHFV Gc, while Gc35 may recognize a different epitope in Gc. Cryo-electron microscopy of Gc-Fab complexes indicated that both Gc8 and Gc13 bind to the conserved fusion loop region and Gc13 had stronger interactions with sGc-trimers. This was supported by the ability of Gc13 to block CCHFV GP-mediated membrane fusion. Overall, this study provides new therapeutic strategies to treat CCHF and new insights into the interaction between antibodies with CCHFV Gc proteins.
History
DepositionJun 3, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36407.png

Downloads & links

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Map

FileDownload / File: emd_36407.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 384 pix.
= 364.8 Å		0.95 Å/pix.
x 384 pix.
= 364.8 Å		0.95 Å/pix.
x 384 pix.
= 364.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-4.352479 - 4.776054
Average (Standard dev.)-0.00003109673 (±0.051409338)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 364.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36407_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36407_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CCHFV envelope protein Gc-Gc13 complex

EntireName: CCHFV envelope protein Gc-Gc13 complex
Components
  • Complex: CCHFV envelope protein Gc-Gc13 complex
    • Protein or peptide: Glycoprotein C,CCHFV Gc fusion loops
    • Protein or peptide: Mouse antibody Gc13 heavy chain
    • Protein or peptide: Mouse antibody Gc13 light chain

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Supramolecule #1: CCHFV envelope protein Gc-Gc13 complex

SupramoleculeName: CCHFV envelope protein Gc-Gc13 complex / 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,CCHFV Gc fusion loops

MacromoleculeName: Glycoprotein C,CCHFV Gc fusion loops / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Crimean-Congo hemorrhagic fever orthonairovirus
Molecular weightTheoretical: 65.880789 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 NSTCTAKASR GSGGMKQIED KIEEILSKIY HIENEIARIK KLIGEG SGG SRGPFEGKPI PNPLLGLDST RTGHHHHHH

UniProtKB: Envelopment polyprotein

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Macromolecule #2: Mouse antibody Gc13 heavy chain

MacromoleculeName: Mouse antibody Gc13 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.931342 KDa
SequenceString:
QVQLQQSGPE VVRPGVSVKI SCKGSGYTFT DYATHWVKQS HVKSLEWIGV ISTYNGETDC NQKFKGKATM TVDKSSSTAY MELARLTSE DSAIYYCANG YYQAMDYWGQ GTSVTVSS

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Macromolecule #3: Mouse antibody Gc13 light chain

MacromoleculeName: Mouse antibody Gc13 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.818041 KDa
SequenceString:
DIQMTQTPSS LSASLGDRVT ISCRASQDIS NYLNWYQQRP DGTLKLLIYY TSRLHSGVPS RFSGSGSGTD YSLTISNLEQ EDIATYFCQ QGSTLPWTFG GGTKLEIK

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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: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 387809
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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