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- EMDB-26841: Atomic model of the partial VSV nucleocapsid -

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Basic information

Entry
Database: EMDB / ID: EMD-26841
TitleAtomic model of the partial VSV nucleocapsid
Map dataCryoEM density map of partial VSV nucleocapsid.
Sample
  • Virus: Vesicular stomatitis virus
    • Protein or peptide: Nucleoprotein
    • RNA: RNA
    • Protein or peptide: Matrix protein
KeywordsVesicular stomatitis virus / Nucleocapsid / Matrix protein M / Nucleocapsid protein N / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


RNA replication / host cell endomembrane system / helical viral capsid / viral transcription / endomembrane system / viral nucleocapsid / host cell cytoplasm / structural constituent of virion / ribonucleoprotein complex / viral envelope ...RNA replication / host cell endomembrane system / helical viral capsid / viral transcription / endomembrane system / viral nucleocapsid / host cell cytoplasm / structural constituent of virion / ribonucleoprotein complex / 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 virus
Methodhelical reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsZhou K / Si Z / Ge P / Tsao J / Luo M / Zhou ZH
Funding support United States, 2 items
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, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26841.png

Downloads & links

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Map

FileDownload / File: emd_26841.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM density map of partial VSV nucleocapsid.
Voxel sizeX=Y=Z: 1.325 Å
Density
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.16113544 - 0.22126201
Average (Standard dev.)0.00097635423 (±0.013661966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 212.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_26841_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_26841_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 : Vesicular stomatitis virus

EntireName: Vesicular stomatitis virus
Components
  • Virus: Vesicular stomatitis virus
    • Protein or peptide: Nucleoprotein
    • RNA: RNA
    • Protein or peptide: Matrix protein

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Supramolecule #1: Vesicular stomatitis virus

SupramoleculeName: Vesicular stomatitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 11276 / Sci species name: Vesicular stomatitis virus / Sci species strain: San Juan / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 600 KDa
Virus shellShell ID: 1 / Name: Helical nucleocapsid / Diameter: 700.0 Å

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Vesicular stomatitis virus / Strain: San Juan
Molecular weightTheoretical: 47.463949 KDa
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 #3: Matrix protein

MacromoleculeName: Matrix protein / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Vesicular stomatitis virus
Molecular weightTheoretical: 26.228188 KDa
SequenceString: MSSFKKILGL SSKSHKKSKK LGLPPPYDES SPMEIQPSAP LSNDFFGMED MDLYDKDSLR YEKFRFMLKM TVRSNKPFRS YDDVTAAVS QWDNSYIGMV GKRPFYKIIA LIGSSHLQAT PAVLADLNQP EYYATLTGRC FLPHRLGLIP PMFNVSETFR K PFNIGIYK ...String:
MSSFKKILGL SSKSHKKSKK LGLPPPYDES SPMEIQPSAP LSNDFFGMED MDLYDKDSLR YEKFRFMLKM TVRSNKPFRS YDDVTAAVS QWDNSYIGMV GKRPFYKIIA LIGSSHLQAT PAVLADLNQP EYYATLTGRC FLPHRLGLIP PMFNVSETFR K PFNIGIYK GTLDFTFTVS DDESNEKVPH VWEYMNPKYQ SQIQKEGLKF GLILSKKATG TWVLDQLSPF K

UniProtKB: Matrix protein

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Macromolecule #2: RNA

MacromoleculeName: RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Vesicular stomatitis virus / Strain: San Juan
Molecular weightTheoretical: 116.603883 KDa
SequenceString: UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU U UUUUUUUU ...String:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU U UUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UU UUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUU UUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUU

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4 / Details: PBS buffer
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 2-44 / Number grids imaged: 1 / Number real images: 2008 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 75.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 1.42 Å
Applied symmetry - Helical parameters - Δ&Phi: -10.14 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION
Details: Additional sub-particle reconstruction was carried out after class3D of helices.
Number images used: 23207
Segment selectionNumber selected: 7732
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2wyy

Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial model
PDB IDChain

2wyy

chain_id: A, source_name: PDB, initial_model_type: experimental model

2w2r

chain_id: A, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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