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- PDB-7umk: Structure of vesicular stomatitis virus (helical reconstruction, ... -

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Basic information

Entry
Database: PDB / ID: 7umk
TitleStructure of vesicular stomatitis virus (helical reconstruction, 4.1 A resolution)
Components
  • Matrix protein
  • Nucleoprotein
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsVIRUS / Vesicular stomatitis virus / bullet-shaped particle / Rhrabdovirus / nucleocapsid / helical reconstruction / cryo electron microscopy / nucleoprotein / matrix protein / RNA / assembly
Function / homology
Function and homology information


symbiont-mediated perturbation of host microtubule cytoskeleton / symbiont-mediated suppression of host transcription initiation from RNA polymerase II promoter / RNA replication / host cell nuclear membrane / phosphorylation / helical viral capsid / viral budding via host ESCRT complex / viral transcription / symbiont-mediated suppression of host mRNA export from nucleus / viral nucleocapsid ...symbiont-mediated perturbation of host microtubule cytoskeleton / symbiont-mediated suppression of host transcription initiation from RNA polymerase II promoter / RNA replication / host cell nuclear membrane / phosphorylation / helical viral capsid / viral budding via host ESCRT complex / viral transcription / symbiont-mediated suppression of host mRNA export from nucleus / viral nucleocapsid / structural constituent of virion / host cell cytoplasm / ribonucleoprotein complex / viral envelope / 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
RNA / Matrix protein / Nucleoprotein
Similarity search - Component
Biological speciesVesicular stomatitis Indiana virus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsJenni, S. / Horwitz, J.A. / Bloyet, L.-M. / Whelan, S.P.J. / Harrison, S.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)R37-AI1059371 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)R01-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, J.A. / Bloyet, L.-M. / Whelan, S.P.J. / Harrison, S.C.
History
DepositionApr 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Matrix protein
C: Matrix protein
R: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)102,3814
Polymers102,3814
Non-polymers00
Water00
1
A: Nucleoprotein
B: Matrix protein
C: Matrix protein
R: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
x 144


Theoretical massNumber of molelcules
Total (without water)14,742,806576
Polymers14,742,806576
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
helical symmetry operation143
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 144 / Rise per n subunits: 1.34094 Å / Rotation per n subunits: -9.3516 °)

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Components

#1: Protein Nucleoprotein / NP / Nucleocapsid protein / Protein N


Mass: 47463.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P03521
#2: Protein Matrix protein / M protein


Mass: 26103.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P03519
#3: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 2710.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus / Production host: Mesocricetus auratus (golden hamster)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Vesicular stomatitis Indiana virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Vesicular stomatitis Indiana virus
Source (recombinant)Organism: Mesocricetus auratus (golden hamster)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -9.3516 ° / Axial rise/subunit: 1.34094 Å / Axial symmetry: C1
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21530 / Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Space: REAL

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