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- EMDB-52152: Cryo-EM structure of VSV-Indiana (MUDD-SUMMERS strain) glycoprote... -

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Basic information

Entry
Database: EMDB / ID: EMD-52152
TitleCryo-EM structure of VSV-Indiana (MUDD-SUMMERS strain) glycoprotein under its acidic conformation
Map data
Sample
  • Virus: VSv (virus)
    • Protein or peptide: Glycoprotein
KeywordsMembrane fusion - virale entry - Rhabdoviruses / VIRAL PROTEIN
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 / VSv (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsAlbertini A / Minoves MJ / OuldAli M / Gaudin Y / Schoehn G / Zarkadas E
Funding support France, 1 items
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 MJ / OuldAli M / Gaudin Y / Schoehn G / Zarkadas E
History
DepositionNov 20, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52152.png

Downloads & links

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Map

FileDownload / File: emd_52152.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 336. Å		1.05 Å/pix.
x 320 pix.
= 336. Å		1.05 Å/pix.
x 320 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.978431 - 3.4501903
Average (Standard dev.)-0.00031087562 (±0.05689656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52152_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52152_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : VSv

EntireName: VSv (virus)
Components
  • Virus: VSv (virus)
    • Protein or peptide: Glycoprotein

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Supramolecule #1: VSv

SupramoleculeName: VSv / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11276 / Sci species name: VSv / Sci species strain: Mudd-summer / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: VSV (virus) / Strain: Mudd-summer
Molecular weightTheoretical: 57 MDa

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Macromolecule #1: Glycoprotein

MacromoleculeName: Glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vesicular stomatitis virus
Molecular weightTheoretical: 55.722012 KDa
Recombinant expressionOrganism: Vesicular stomatitis virus
SequenceString: KFTIVFPHNQ KGNWKNVPSN YHYCPSSSDL NWHNDLIGTA LQVKMPKSHK AIQADGWMCH ASKWVTTCDF RWYGPKYITH SIRSFTPSV EQCKESIEQT KQGTWLNPGF PPQSCGYATV TDAEAVIVQV TPHHVLVDEY TGEWVDSQFI NGKCSNYICP T VHNSTTWH ...String:
KFTIVFPHNQ KGNWKNVPSN YHYCPSSSDL NWHNDLIGTA LQVKMPKSHK AIQADGWMCH ASKWVTTCDF RWYGPKYITH SIRSFTPSV EQCKESIEQT KQGTWLNPGF PPQSCGYATV TDAEAVIVQV TPHHVLVDEY TGEWVDSQFI NGKCSNYICP T VHNSTTWH SDYKVKGLCD SNLISMDITF FSEDGELSSL GKEGTGFRSN YFAYETGGKA CKMQYCKHWG VRLPSGVWFE MA DKDLFAA ARFPECPEGS SISAPSQTSV DVSLIQDVER ILDYSLCQET WSKIRAGLPI SPVDLSYLAP KNPGTGPAFT IIN GTLKYF ETRYIRVDIA APILSRMVGM ISGTTTEREL WDDWAPYEDV EIGPNGVLRT SSGYKFPLYM IGHGMLDSDL HLSS KAQVF EHPHIQDAAS QLPDDESLFF GDTGLSKNPI ELVEGWFSSW KSSIASFFFI IGLIIGLFLV LRVGIHLCIK LKHTK KRQI YTDIEMNRLG K

UniProtKB: Glycoprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 8
GridModel: UltrAuFoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131840
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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