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- PDB-7fgf: Cryo-EM structure of CCHFV envelope protein Gc in postfusion conf... -

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Basic information

Entry
Database: PDB / ID: 7fgf
TitleCryo-EM structure of CCHFV envelope protein Gc in postfusion conformation
ComponentsGlycoprotein C
KeywordsVIRAL PROTEIN / CCHFV / envelope protein / postfusion / Bunyavirus
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLi, N. / Rao, G. / Fu, Y. / Cao, S.
Funding support China, 1items
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, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

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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
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "A"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSILEC1 - 432
d_21ens_1LYSILEB1 - 432
d_31ens_1LYSILEA1 - 432

NCS oper:
IDCodeMatrixVector
1given(-0.500798712384, 0.865563764304, 0.000139992346704), (-0.865563771365, -0.500798719415, 1.82144370401E-5), (8.58737446466E-5, -0.000112050536959, 0.999999990035)26.9985565412, 94.8885327798, -0.00101162524459
2given(-0.499542266178, -0.866289515235, -9.81093168996E-6), (0.866289515288, -0.499542266172, -3.15808918957E-6), (-2.16515549656E-6, -1.00767062888E-5, 0.999999999947)95.6490325304, 24.0616187376, 0.00420634603286

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Components

#1: Protein Glycoprotein C / Gc / 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
Strain: IbAr10200 / Gene: GP / Cell line (production host): Schneider S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8JSZ3
Has protein modificationY

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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 FIELD
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: cryoSPARC / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 187292 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 43.91 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00610353
ELECTRON MICROSCOPYf_angle_d0.75814022
ELECTRON MICROSCOPYf_dihedral_angle_d21.6291356
ELECTRON MICROSCOPYf_chiral_restr0.0491614
ELECTRON MICROSCOPYf_plane_restr0.0051755
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CELECTRON MICROSCOPYNCS constraints0.00070759458673
ens_1d_3CELECTRON MICROSCOPYNCS constraints0.00070097247401

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