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- EMDB-52169: Cryo-EM structure of VSV-Indiana glycoprotein (MUDD-SUMMERS strai... -

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Basic information

Entry
Database: EMDB / ID: EMD-52169
TitleCryo-EM structure of VSV-Indiana glycoprotein (MUDD-SUMMERS strain) in its pre-fusion conformation in complex with 8G5F11 Fab
Map data
Sample
  • Virus: VSV (virus)
    • Protein or peptide: Glycoprotein
    • Protein or peptide: 8G5F11 VL
    • Protein or peptide: 8G5F11 VH
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 / Mus sp. (mice) / VSV (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 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 structures of VSV G alone and in complex with a neutralizing antibody
Authors: Albertini A / Minoves MJ / OuldAli M / Gaudin Y / Schoehn G / Zarkadas E
History
DepositionNov 21, 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_52169.png

Downloads & links

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Map

FileDownload / File: emd_52169.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 300 pix.
= 343.5 Å		1.15 Å/pix.
x 300 pix.
= 343.5 Å		1.15 Å/pix.
x 300 pix.
= 343.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.145 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-1.7909777 - 2.6570072
Average (Standard dev.)0.0007276649 (±0.054198682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 343.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52169_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_52169_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
    • Protein or peptide: 8G5F11 VL
    • Protein or peptide: 8G5F11 VH

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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
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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Macromolecule #2: 8G5F11 VL

MacromoleculeName: 8G5F11 VL / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus sp. (mice)
Molecular weightTheoretical: 23.858164 KDa
Recombinant expressionOrganism: Eukaryota (eukaryotes)
SequenceString: DIVMTQSHKF MSTSVGDRVS ITCKASQDVD NDVAWYQQKP GQSPKLLIYW ASTRHTGVPD RFTGSGSGTD FTLTISDVQS EDLSDYFCQ QYSSYPFTFG GGTRLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIVMTQSHKF MSTSVGDRVS ITCKASQDVD NDVAWYQQKP GQSPKLLIYW ASTRHTGVPD RFTGSGSGTD FTLTISDVQS EDLSDYFCQ QYSSYPFTFG GGTRLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

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Macromolecule #3: 8G5F11 VH

MacromoleculeName: 8G5F11 VH / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus sp. (mice)
Molecular weightTheoretical: 24.806494 KDa
Recombinant expressionOrganism: Eukaryota (eukaryotes)
SequenceString: DVQLQESGPD LVKPSQSLSL TCTVTGYSIT SGYSWHWNRQ FPGNKLEWMG YIHYSGLTNY NPSLKSRISI TRHTSKNQFF LQLNSVTTE DTATYYCVRG GYDGRDYYAM DFWGQGTSVT VSSAKTTAPS VYPLAPVCGD TTGSSVTLGC LVKGYFPEPV T LTWNSGSL ...String:
DVQLQESGPD LVKPSQSLSL TCTVTGYSIT SGYSWHWNRQ FPGNKLEWMG YIHYSGLTNY NPSLKSRISI TRHTSKNQFF LQLNSVTTE DTATYYCVRG GYDGRDYYAM DFWGQGTSVT VSSAKTTAPS VYPLAPVCGD TTGSSVTLGC LVKGYFPEPV T LTWNSGSL SSGVHTFPAV LQSDLYTLSS SVTVPSSTWP SQTVTCSVAH PASSTTVDKK LEPSGPISTI N

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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

Concentration0.83 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 GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 294045
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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