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- PDB-8jkd: Cryo-EM structure of CCHFV envelope protein Gc trimer in complex ... -

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Basic information

Entry
Database: PDB / ID: 8jkd
TitleCryo-EM structure of CCHFV envelope protein Gc trimer in complex with Gc13 Fab
ComponentsGlycoprotein C
KeywordsVIRAL PROTEIN / CCHFV / envelope protein / postfusion / Bunyavirus
Function / homology
Function and homology information


host cell Golgi membrane / virus-mediated perturbation of host defense response / 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, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Nairovirus M polyprotein-like / Nairovirus GP38 / : ...: / : / : / : / Nairovirus, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Nairovirus M polyprotein-like / Nairovirus GP38 / : / Hantavirus glycoprotein Gc, C-terminal / Hantavirus glycoprotein Gc / Hantavirus glycoprotein Gc, N-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus strain IbAr10200
Crimean-Congo hemorrhagic fever virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsChong, T. / Cao, S.
Funding support China, 1items
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 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoprotein C
B: Glycoprotein C
C: Glycoprotein C


Theoretical massNumber of molelcules
Total (without water)197,4293
Polymers197,4293
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Glycoprotein C / Gc / 75 kDa protein / Glycoprotein G1


Mass: 65809.711 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus strain IbAr10200, (gene. exp.) Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)
Strain: Nigeria/IbAr10200/1970 / Gene: GP / Cell line (production host): Schneider S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8JSZ3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CCHFV envelope protein Gc / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Crimean-Congo hemorrhagic fever virus strain IbAr10200
Source (recombinant)Organism: Drosophila melanogaster (fruit fly) / Cell: Schneider S2 cells
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: cryoSPARC / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 465995 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 38.06 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311203
ELECTRON MICROSCOPYf_angle_d0.61815185
ELECTRON MICROSCOPYf_dihedral_angle_d5.6391477
ELECTRON MICROSCOPYf_chiral_restr0.0461720
ELECTRON MICROSCOPYf_plane_restr0.0051921

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