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- PDB-6f9d: Model of the Rift Valley fever virus glycoprotein hexamer type 2 -

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Basic information

Entry
Database: PDB / ID: 6f9d
TitleModel of the Rift Valley fever virus glycoprotein hexamer type 2
Components(Glycoprotein) x 2
KeywordsVIRUS / enveloped virus / RVFV / glycoprotein / fusion protein
Function / homology
Function and homology information


host cell mitochondrial outer membrane / symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host apoptosis / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / 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 nonstructural NS-M / M polyprotein precursor, phlebovirus / Phlebovirus nonstructural protein NS-M / 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 / Envelopment polyprotein / Envelopment polyprotein
Similarity search - Component
Biological speciesRift valley fever virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.3 Å
AuthorsHalldorsson, S. / Bowden, T.A. / Huiskonen, J.T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council649053 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Shielding and activation of a viral membrane fusion protein.
Authors: Steinar Halldorsson / Sai Li / Mengqiu Li / Karl Harlos / Thomas A Bowden / Juha T Huiskonen /
Abstract: Entry of enveloped viruses relies on insertion of hydrophobic residues of the viral fusion protein into the host cell membrane. However, the intermediate conformations during fusion remain unknown. ...Entry of enveloped viruses relies on insertion of hydrophobic residues of the viral fusion protein into the host cell membrane. However, the intermediate conformations during fusion remain unknown. Here, we address the fusion mechanism of Rift Valley fever virus. We determine the crystal structure of the Gn glycoprotein and fit it with the Gc fusion protein into cryo-electron microscopy reconstructions of the virion. Our analysis reveals how the Gn shields the hydrophobic fusion loops of the Gc, preventing premature fusion. Electron cryotomography of virions interacting with membranes under acidic conditions reveals how the fusogenic Gc is activated upon removal of the Gn shield. Repositioning of the Gn allows extension of Gc and insertion of fusion loops in the outer leaflet of the target membrane. These data show early structural transitions that enveloped viruses undergo during host cell entry and indicate that analogous shielding mechanisms are utilized across diverse virus families.
History
DepositionDec 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Glycoprotein
B: Glycoprotein
C: Glycoprotein
D: Glycoprotein
E: Glycoprotein
F: Glycoprotein
G: Glycoprotein
H: Glycoprotein
I: Glycoprotein
J: Glycoprotein
K: Glycoprotein
L: Glycoprotein


Theoretical massNumber of molelcules
Total (without water)490,94712
Polymers490,94712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area32140 Å2
ΔGint-68 kcal/mol
Surface area195830 Å2
MethodPISA

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Components

#1: Protein
Glycoprotein


Mass: 34968.902 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift valley fever virus / Production host: Homo sapiens (human) / References: UniProt: A2T085, UniProt: P21401*PLUS
#2: Protein
Glycoprotein


Mass: 46855.570 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift valley fever virus / Production host: Homo sapiens (human) / References: UniProt: A2T072, UniProt: P21401*PLUS

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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: Rift Valley fever virus / Type: VIRUS / Details: Cultured in Vero cells / Entity ID: all / Source: NATURAL
Source (natural)Organism: Rift Valley fever virus
Details of virusEmpty: NO / Enveloped: YES / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Glycoprotein shell / Diameter: 1100 nm / Triangulation number (T number): 12
Buffer solutionpH: 7.5 / Details: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Fixed with 0.2% v/v formaldehyde in PBS
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 22 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1ETHANparticle selection
4CTFFINDCTF correctionDetermination
5RELIONCTF correctionCorrection
8MDFFmodel fitting
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
13RELION1.43D reconstruction
20PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 13.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2995 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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