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- PDB-7xym: The pre-fusion structure of Thogotovirus dhori envelope glycoprotein -

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Basic information

Entry
Database: PDB / ID: 7xym
TitleThe pre-fusion structure of Thogotovirus dhori envelope glycoprotein
ComponentsEnvelope glycoprotein
KeywordsSTRUCTURAL PROTEIN / Viral surface protein
Function / homologyBaculovirus Gp64, envelope glycoprotein / Baculovirus gp64 envelope glycoprotein / symbiont-mediated perturbation of host process / viral envelope / virion membrane / membrane / Envelope glycoprotein
Function and homology information
Biological speciesDhori thogotovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsShan, Y.Y. / Zhang, M.F. / Pei, D.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2017YFA0504100 China
CitationJournal: To Be Published
Title: Pre- and post-fusion class III glycoprotein structures reveal viral fusion mechanism
Authors: Shan, Y.Y. / Zhang, M.F. / Pei, D.Q.
History
DepositionJun 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein
B: Envelope glycoprotein
C: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)176,0233
Polymers176,0233
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Envelope glycoprotein


Mass: 58674.496 Da / Num. of mol.: 3 / Mutation: G74S, N298D, K442E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dhori thogotovirus / Strain: Indian/1313/61 / Gene: P4 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P27427
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: Thogotovirus dhori envelope glycoprotein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Dhori thogotovirus
Source (recombinant)Organism: Homo sapiens (human)
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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 155000 / Symmetry type: POINT

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