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Yorodumi- EMDB-26602: Structure of vesicular stomatitis virus (helical reconstruction, ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26602 | |||||||||
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Title | Structure of vesicular stomatitis virus (helical reconstruction, 4.1 A resolution) | |||||||||
Map data | Reconstructed, symmetrized, boxed, locscale, sharpen_map | |||||||||
Sample |
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Keywords | Vesicular stomatitis virus / bullet-shaped particle / Rhrabdovirus / nucleocapsid / helical reconstruction / cryo electron microscopy / nucleoprotein / matrix protein / RNA / assembly / VIRUS | |||||||||
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 / phosphorylation / symbiont-mediated suppression of host mRNA export from nucleus / viral nucleocapsid / 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 / phosphorylation / symbiont-mediated suppression of host mRNA export from nucleus / viral nucleocapsid / host cell cytoplasm / structural constituent of virion / ribonucleoprotein complex / viral envelope / apoptotic process / virion membrane / RNA binding / membrane Similarity search - Function | |||||||||
Biological species | Vesicular stomatitis Indiana virus | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Jenni S / Horwitz JA / Bloyet L-M / Whelan SPJ / Harrison SC | |||||||||
Funding support | United States, 2 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26602.map.gz | 84 MB | EMDB map data format | |
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Header (meta data) | emd-26602-v30.xml emd-26602.xml | 26.3 KB 26.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26602_fsc.xml | 16.4 KB | Display | FSC data file |
Images | emd_26602.png | 161.5 KB | ||
Masks | emd_26602_msk_1.map | 89.5 MB | Mask map | |
Filedesc metadata | emd-26602.cif.gz | 6.3 KB | ||
Others | emd_26602_additional_1.map.gz emd_26602_additional_2.map.gz emd_26602_additional_3.map.gz emd_26602_additional_4.map.gz emd_26602_half_map_1.map.gz emd_26602_half_map_2.map.gz | 1021.4 MB 1022.4 MB 1020.9 MB 70 MB 70 MB 69.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26602 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26602 | HTTPS FTP |
-Validation report
Summary document | emd_26602_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_26602_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_26602_validation.xml.gz | 15 KB | Display | |
Data in CIF | emd_26602_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26602 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26602 | HTTPS FTP |
-Related structure data
Related structure data | 7umkMC 7umlC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26602.map.gz / Format: CCP4 / Size: 89.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Reconstructed, symmetrized, boxed, locscale, sharpen_map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26602_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Reconstructed, symmetrized
File | emd_26602_additional_1.map | ||||||||||||
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Annotation | Reconstructed, symmetrized | ||||||||||||
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Density Histograms |
-Additional map: Half map 1, reconstructed, symmetrized
File | emd_26602_additional_2.map | ||||||||||||
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Annotation | Half map 1, reconstructed, symmetrized | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half map 2, reconstructed, symmetrized
File | emd_26602_additional_3.map | ||||||||||||
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Annotation | Half map 2, reconstructed, symmetrized | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Reconstructed, symmetrized, boxed
File | emd_26602_additional_4.map | ||||||||||||
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Annotation | Reconstructed, symmetrized, boxed | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1, reconstructed, symmetrized, boxed
File | emd_26602_half_map_1.map | ||||||||||||
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Annotation | Half map 1, reconstructed, symmetrized, boxed | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2, reconstructed, symmetrized, boxed
File | emd_26602_half_map_2.map | ||||||||||||
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Annotation | Half map 2, reconstructed, symmetrized, boxed | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Vesicular stomatitis Indiana virus
Entire | Name: Vesicular stomatitis Indiana virus |
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Components |
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-Supramolecule #1: Vesicular stomatitis Indiana virus
Supramolecule | Name: 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
Macromolecule | Name: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vesicular stomatitis Indiana virus |
Molecular weight | Theoretical: 47.463949 KDa |
Recombinant expression | Organism: Mesocricetus auratus (golden hamster) |
Sequence | String: 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 |
-Macromolecule #2: Matrix protein
Macromolecule | Name: Matrix protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vesicular stomatitis Indiana virus |
Molecular weight | Theoretical: 26.103055 KDa |
Recombinant expression | Organism: Mesocricetus auratus (golden hamster) |
Sequence | String: 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 |
-Macromolecule #3: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
Macromolecule | Name: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Vesicular stomatitis Indiana virus |
Molecular weight | Theoretical: 2.710535 KDa |
Sequence | String: UUUUUUUUU |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | PDB-7umk: |