[English] 日本語
Yorodumi
- PDB-7umk: Structure of vesicular stomatitis virus (helical reconstruction, ... -

+
Open data


ID or keywords:

Loading...

-
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 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 / phosphorylation / host cell cytoplasm ...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 / phosphorylation / host cell cytoplasm / structural constituent of virion / ribonucleoprotein complex / viral envelope / apoptotic process / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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 °)

-
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)

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more