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- PDB-7uws: Atomic model of the partial VSV nucleocapsid -

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Basic information

Entry
Database: PDB / ID: 7uws
TitleAtomic model of the partial VSV nucleocapsid
Components
  • Matrix protein
  • Nucleoprotein
  • RNA
KeywordsVIRAL PROTEIN/RNA / Vesicular stomatitis virus / Nucleocapsid / Matrix protein M / Nucleocapsid protein N / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


RNA replication / host cell nuclear membrane / helical viral capsid / viral budding via host ESCRT complex / viral transcription / viral nucleocapsid / structural constituent of virion / host cell cytoplasm / ribonucleoprotein complex / viral envelope / RNA binding
Similarity search - Function
Vesiculovirus matrix / VSV matrix superfamily / Vesiculovirus matrix protein / Rhabdovirus nucleoprotein-like / Nucleoprotein / Rhabdovirus nucleoprotein-like fold / Rhabdovirus nucleocapsid protein like domain / Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal ...Vesiculovirus matrix / VSV matrix superfamily / Vesiculovirus matrix protein / Rhabdovirus nucleoprotein-like / Nucleoprotein / Rhabdovirus nucleoprotein-like fold / Rhabdovirus nucleocapsid protein like domain / Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Matrix protein / Nucleoprotein
Similarity search - Component
Biological speciesVesicular stomatitis virus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsZhou, K. / Si, Z. / Ge, P. / Tsao, J. / Luo, M. / Zhou, Z.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)GM071940 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)AI094386 United States
CitationJournal: Nat Commun / Year: 2022
Title: Atomic model of vesicular stomatitis virus and mechanism of assembly.
Authors: Kang Zhou / Zhu Si / Peng Ge / Jun Tsao / Ming Luo / Z Hong Zhou /
Abstract: Like other negative-strand RNA viruses (NSVs) such as influenza and rabies, vesicular stomatitis virus (VSV) has a three-layered organization: a layer of matrix protein (M) resides between the ...Like other negative-strand RNA viruses (NSVs) such as influenza and rabies, vesicular stomatitis virus (VSV) has a three-layered organization: a layer of matrix protein (M) resides between the glycoprotein (G)-studded membrane envelope and the nucleocapsid, which is composed of the nucleocapsid protein (N) and the encapsidated genomic RNA. Lack of in situ atomic structures of these viral components has limited mechanistic understanding of assembling the bullet-shaped virion. Here, by cryoEM and sub-particle reconstruction, we have determined the in situ structures of M and N inside VSV at 3.47 Å resolution. In the virion, N and M sites have a stoichiometry of 1:2. The in situ structures of both N and M differ from their crystal structures in their N-terminal segments and oligomerization loops. N-RNA, N-N, and N-M-M interactions govern the formation of the capsid. A double layer of M contributes to packaging of the helical nucleocapsid: the inner M (IM) joins neighboring turns of the N helix, while the outer M (OM) contacts G and the membrane envelope. The pseudo-crystalline organization of G is further mapped by cryoET. The mechanism of VSV assembly is delineated by the network interactions of these viral components.
History
DepositionMay 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 12, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
F: Nucleoprotein
G: Nucleoprotein
H: RNA
J: Matrix protein
K: Matrix protein
L: Matrix protein
M: Matrix protein
N: Matrix protein
O: Matrix protein
P: Matrix protein
Q: Matrix protein
R: Matrix protein
S: Matrix protein
T: Matrix protein
U: Matrix protein


Theoretical massNumber of molelcules
Total (without water)763,59020
Polymers763,59020
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 47463.949 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Vesicular stomatitis virus / Strain: San Juan / References: UniProt: P03521
#2: RNA chain RNA


Mass: 116603.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vesicular stomatitis virus / Strain: San Juan
#3: Protein
Matrix protein


Mass: 26228.188 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Vesicular stomatitis virus / References: UniProt: I7DGS2

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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 virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.6 MDa / Experimental value: NO
Source (natural)Organism: Vesicular stomatitis virus / Strain: San Juan
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Helical nucleocapsid / Diameter: 700 nm
Buffer solutionpH: 7.4 / Details: PBS buffer
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 75 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2008
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Used frames/image: 2-44

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9Cootmodel refinement
10PHENIXmodel refinement
13RELIONclassification
14RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -10.14 ° / Axial rise/subunit: 1.42 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 7732
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23207
Details: Additional sub-particle reconstruction was carried out after class3D of helices.
Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model building

3D fitting-ID: 1 / Pdb chain-ID: A / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeInitial refinement model-ID
12WYY

2wyy

2WYY1
22W2R

2w2r

2W2R2

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