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- PDB-9hgn: Cryo-EM structure of VSV-Indiana (MUDD-SUMMERS strain) glycoprote... -

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Basic information

Entry
Database: PDB / ID: 9hgn
TitleCryo-EM structure of VSV-Indiana (MUDD-SUMMERS strain) glycoprotein under its acidic conformation
ComponentsGlycoprotein
KeywordsVIRAL PROTEIN / Membrane fusion - virale entry - Rhabdoviruses
Function / homology
Function and homology information


host cell membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane / metal ion binding / membrane
Similarity search - Function
: / Rhabdovirus spike glycoprotein G central domain / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein fusion domain
Similarity search - Domain/homology
Biological speciesVesicular stomatitis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsAlbertini, A. / Minoves, M.J. / OuldAli, M. / Gaudin, Y. / Schoehn, G. / Zarkadas, E.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-22-CE11-0009-01 France
CitationJournal: To Be Published
Title: Cryo-EM structure of VSV-Indiana (MUDD-SUMMERS strain) glycoprotein under its acidic conformation
Authors: Albertini, A. / Minoves, M.J. / OuldAli, M. / Gaudin, Y. / Schoehn, G. / Zarkadas, E.
History
DepositionNov 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoprotein
B: Glycoprotein
C: Glycoprotein


Theoretical massNumber of molelcules
Total (without water)167,1663
Polymers167,1663
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Glycoprotein


Mass: 55722.012 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis virus / Production host: Vesicular stomatitis virus / References: UniProt: B7UCZ5
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: VSv / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 57 MDa / Experimental value: YES
Source (natural)Organism: VSv (virus) / Strain: Mudd-summer
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: VSV / Strain: Mudd-summer
Buffer solutionpH: 8
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: UltrAuFoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131840 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310434
ELECTRON MICROSCOPYf_angle_d0.58314213
ELECTRON MICROSCOPYf_dihedral_angle_d4.5311371
ELECTRON MICROSCOPYf_chiral_restr0.0431503
ELECTRON MICROSCOPYf_plane_restr0.0061829

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