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- EMDB-26603: Structure of vesicular stomatitis virus (local reconstruction, 3.... -

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Basic information

Entry
Database: EMDB / ID: EMD-26603
TitleStructure of vesicular stomatitis virus (local reconstruction, 3.5 A resolution)
Map dataFinal sharpened
Sample
  • Virus: Vesicular stomatitis Indiana virus
    • Protein or peptide: Nucleoprotein
    • Protein or peptide: Matrix proteinViral matrix protein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsVesicular stomatitis virus / bullet-shaped particle / Rhrabdovirus / nucleocapsid / helical reconstruction / cryo electron microscopy / nucleoprotein / matrix protein / RNA / assembly / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


symbiont-mediated suppression of host transcription initiation from RNA polymerase II promoter / RNA replication / host cell nuclear membrane / helical viral capsid / viral budding via host ESCRT complex / viral transcription / symbiont-mediated suppression of host mRNA export from nucleus / viral nucleocapsid / host cell cytoplasm / structural constituent of virion ...symbiont-mediated suppression of host transcription initiation from RNA polymerase II promoter / RNA replication / host cell nuclear membrane / helical viral capsid / viral budding via host ESCRT complex / viral transcription / symbiont-mediated suppression of host mRNA export from nucleus / viral nucleocapsid / host cell cytoplasm / structural constituent of virion / ribonucleoprotein complex / phosphorylation / viral envelope / virion membrane / RNA binding / membrane
Similarity search - Function
Vesiculovirus matrix / VSV matrix superfamily / Vesiculovirus matrix protein / Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein
Similarity search - Domain/homology
Matrix protein / Nucleoprotein
Similarity search - Component
Biological speciesVesicular stomatitis Indiana virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsJenni S / Horwitz JA / Bloyet L-M / Whelan SPJ / Harrison SC
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)AI1059371 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)CA13202 United States
Citation
Journal: Nat Commun / Year: 2022
Title: Visualizing molecular interactions that determine assembly of a bullet-shaped vesicular stomatitis virus particle.
Authors: Simon Jenni / Joshua A Horwitz / Louis-Marie Bloyet / Sean P J Whelan / Stephen C Harrison /
Abstract: Vesicular stomatitis virus (VSV) is a negative-strand RNA virus with a non-segmented genome, closely related to rabies virus. Both have characteristic bullet-like shapes. We report the structure of ...Vesicular stomatitis virus (VSV) is a negative-strand RNA virus with a non-segmented genome, closely related to rabies virus. Both have characteristic bullet-like shapes. We report the structure of intact, infectious VSV particles determined by cryogenic electron microscopy. By compensating for polymorphism among viral particles with computational classification, we obtained a reconstruction of the shaft ("trunk") at 3.5 Å resolution, with lower resolution for the rounded tip. The ribonucleoprotein (RNP), genomic RNA complexed with nucleoprotein (N), curls into a dome-like structure with about eight gradually expanding turns before transitioning into the regular helical trunk. Two layers of matrix (M) protein link the RNP with the membrane. Radial inter-layer subunit contacts are fixed within single RNA-N-M1-M2 modules, but flexible lateral and axial interactions allow assembly of polymorphic virions. Together with published structures of recombinant N in various states, our results suggest a mechanism for membrane-coupled self-assembly of VSV and its relatives.
#1: Journal: Biorxiv / Year: 2022
Title: Visualizing Molecular Interactions that Determine Assembly of a Bullet-Shaped Vesicular Stomatitis Virus Particle
Authors: Jenni S / Horwitz JA / Bloyet L-M / Whelan SPJ / Harrison SC
History
DepositionApr 7, 2022-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26603.png

Downloads & links

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Map

FileDownload / File: emd_26603.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-46.769669999999998 - 62.831817999999998
Average (Standard dev.)0.053066146 (±1.3581259)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26603_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Final

Fileemd_26603_additional_1.map
AnnotationFinal
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_26603_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_26603_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vesicular stomatitis Indiana virus

EntireName: Vesicular stomatitis Indiana virus
Components
  • Virus: Vesicular stomatitis Indiana virus
    • Protein or peptide: Nucleoprotein
    • Protein or peptide: Matrix proteinViral matrix protein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')

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Supramolecule #1: Vesicular stomatitis Indiana virus

SupramoleculeName: Vesicular stomatitis Indiana virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11277 / Sci species name: Vesicular stomatitis Indiana virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vesicular stomatitis Indiana virus
Molecular weightTheoretical: 47.463949 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: MSVTVKRIID NTVIVPKLPA NEDPVEYPAD YFRKSKEIPL YINTTKSLSD LRGYVYQGLK SGNVSIIHVN SYLYGALKDI RGKLDKDWS SFGINIGKAG DTIGIFDLVS LKALDGVLPD GVSDASRTSA DDKWLPLYLL GLYRVGRTQM PEYRKKLMDG L TNQCKMIN ...String:
MSVTVKRIID NTVIVPKLPA NEDPVEYPAD YFRKSKEIPL YINTTKSLSD LRGYVYQGLK SGNVSIIHVN SYLYGALKDI RGKLDKDWS SFGINIGKAG DTIGIFDLVS LKALDGVLPD GVSDASRTSA DDKWLPLYLL GLYRVGRTQM PEYRKKLMDG L TNQCKMIN EQFEPLVPEG RDIFDVWGND SNYTKIVAAV DMFFHMFKKH ECASFRYGTI VSRFKDCAAL ATFGHLCKIT GM STEDVTT WILNREVADE MVQMMLPGQE IDKADSYMPY LIDFGLSSKS PYSSVKNPAF HFWGQLTALL LRSTRARNAR QPD DIEYTS LTTAGLLYAY AVGSSADLAQ QFCVGDNKYT PDDSTGGLTT NAPPQGRDVV EWLGWFEDQN RKPTPDMMQY AKRA VMSLQ GLREKTIGKY AKSEFDK

UniProtKB: Nucleoprotein

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Macromolecule #2: Matrix protein

MacromoleculeName: Matrix protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vesicular stomatitis Indiana virus
Molecular weightTheoretical: 26.103055 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: MSSLKKILGL KGKGKKSKKL GIAPPPYEED TSMEYAPSAP IDKSYFGVDE MDTYDPNQLR YEKFFFTVKM TVRSNRPFRT YSDVAAAVS HWDHMYIGMA GKRPFYKILA FLGSSNLKAT PAVLADQGQP EYHAHCEGRA YLPHRMGKTP PMLNVPEHFR R PFNIGLYK ...String:
MSSLKKILGL KGKGKKSKKL GIAPPPYEED TSMEYAPSAP IDKSYFGVDE MDTYDPNQLR YEKFFFTVKM TVRSNRPFRT YSDVAAAVS HWDHMYIGMA GKRPFYKILA FLGSSNLKAT PAVLADQGQP EYHAHCEGRA YLPHRMGKTP PMLNVPEHFR R PFNIGLYK GTIELTMTIY DDESLEAAPM IWDHFNSSKF SDFREKALMF GLIVEKKASG AWVLDSISHF K

UniProtKB: Matrix protein

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Macromolecule #3: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Vesicular stomatitis Indiana virus
Molecular weightTheoretical: 3.935198 KDa
SequenceString:
UUUUUUUUUU UUU

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE
DetailsSubparticle reconstruction

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2985175
DetailsSubparticle reconstruction.
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7uml:
Structure of vesicular stomatitis virus (local reconstruction, 3.5 A resolution)

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