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- PDB-9hh9: Cryo-EM structure of VSV-Indiana glycoprotein (MUDD-SUMMERS strai... -

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Basic information

Entry
Database: PDB / ID: 9hh9
TitleCryo-EM structure of VSV-Indiana glycoprotein (MUDD-SUMMERS strain) in its pre-fusion conformation in complex with 8G5F11 Fab
Components
  • 8G5F11 VH
  • 8G5F11 VL
  • Glycoprotein
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 speciesMus sp. (mice)
Vesicular stomatitis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 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 structures of VSV G alone and in complex with a neutralizing antibody
Authors: Albertini, A. / Minoves, M.J. / OuldAli, M. / Gaudin, Y. / Schoehn, G. / Zarkadas, E.
History
DepositionNov 21, 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

Downloads & links

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Assembly

Deposited unit
A: Glycoprotein
B: Glycoprotein
C: Glycoprotein
D: 8G5F11 VL
E: 8G5F11 VH
F: 8G5F11 VL
G: 8G5F11 VH
H: 8G5F11 VL
I: 8G5F11 VH


Theoretical massNumber of molelcules
Total (without water)313,1609
Polymers313,1609
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 natural source / Source: (natural) Vesicular stomatitis virus / References: UniProt: B7UCZ5
#2: Antibody 8G5F11 VL


Mass: 23858.164 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus sp. (mice) / Production host: Eukaryota (eukaryotes)
#3: Antibody 8G5F11 VH


Mass: 24806.494 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus sp. (mice) / Production host: Eukaryota (eukaryotes)
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.: 0.83 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

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 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 K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 294045 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00416129
ELECTRON MICROSCOPYf_angle_d0.7521964
ELECTRON MICROSCOPYf_dihedral_angle_d6.2282148
ELECTRON MICROSCOPYf_chiral_restr0.0482323
ELECTRON MICROSCOPYf_plane_restr0.0062828

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