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- PDB-9t53: Structure of the Vesicular Stomatitis Virus L Protein in Complex ... -

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Basic information

Entry
Database: PDB / ID: 9t53
TitleStructure of the Vesicular Stomatitis Virus L Protein in Complex with the Phosphoprotein and the Nucleoprotein
Components
  • Nucleoprotein
  • Phosphoprotein
  • RNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN / Vesicular stomatitis virus / L protein / P protein / phosphoprotein / nucleoprotein / N protein / single particle analysis / replication / virus / protein complex / N0-P complex / replication complex
Function / homology
Function and homology information


RNA replication / GDP polyribonucleotidyltransferase / RNA 2'-O-methyltransferase activity / RNA folding chaperone / phosphorylation / negative stranded viral RNA replication / helical viral capsid / viral transcription / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / viral genome replication ...RNA replication / GDP polyribonucleotidyltransferase / RNA 2'-O-methyltransferase activity / RNA folding chaperone / phosphorylation / negative stranded viral RNA replication / helical viral capsid / viral transcription / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / viral genome replication / viral nucleocapsid / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ribonucleoprotein complex / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase activity / host cell cytoplasm / metal ion binding / RNA binding / ATP binding
Similarity search - Function
Phosphoprotein, central domain / : / : / Vesiculovirus phosphoprotein / Virus-capping methyltransferase, C-terminal / Phosphoprotein, C-terminal domain, viral / RNA-directed RNA polymerase, rhabdovirus / : / Virus-capping methyltransferase, connector domain / Rhabdovirus nucleocapsid ...Phosphoprotein, central domain / : / : / Vesiculovirus phosphoprotein / Virus-capping methyltransferase, C-terminal / Phosphoprotein, C-terminal domain, viral / RNA-directed RNA polymerase, rhabdovirus / : / Virus-capping methyltransferase, connector domain / Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Phosphoprotein / Nucleoprotein / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesVesicular stomatitis Indiana virus strain San Juan
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
Model detailsRigid-body fitting of L and P(49-106) from 6U1X and N and P(5-32) from 3PMK
AuthorsBloyet, L.M. / Whelan, S.P.J.
Funding support United States, France, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI059371 United States
Agence Nationale de la Recherche (ANR)ANR-23-CE11-0001-01 France
CitationJournal: To Be Published
Title: Structure of the Vesicular Stomatitis Virus L Protein in Complex with the Phosphoprotein and the Nucleoprotein
Authors: Bloyet, L.M. / Whelan, S.P.J.
History
DepositionNov 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: RNA-directed RNA polymerase L
N: Nucleoprotein
P: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,9895
Polymers301,8593
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase


Mass: 241339.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus strain San Juan
Cell line (production host): BSR-T7 / Production host: Mesocricetus auratus (golden hamster)
References: UniProt: P03523, RNA-directed RNA polymerase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides, GDP polyribonucleotidyltransferase, NNS virus cap methyltransferase
#2: 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 strain San Juan
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: P03521
#3: Protein Phosphoprotein / P protein / Protein M1


Mass: 13054.788 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vesicular stomatitis Indiana virus strain San Juan
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: P03520
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1VSIV L:P:N complexCOMPLEXL protein (full-length) in complex with P protein (1-106) and N protein (full-length)#1-#30RECOMBINANT
2L:P complexCOMPLEXL protein (full-length) in complex with a fragment of P (49-106)#1, #31RECOMBINANT
3N0-P complexCOMPLEXN protein (full-length) in complex with a framgent of P (5-32)#2-#31RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.3 MDaNO
210.25 MDaNO
310.05 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Vesicular stomatitis Indiana virus strain San Juan11285
32Vesicular stomatitis Indiana virus strain San Juan11285
43Vesicular stomatitis Indiana virus strain San Juan11285
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Mesocricetus auratus (golden hamster)10036BSR-T7
32Mesocricetus auratus (golden hamster)10036BSR-T7
33Escherichia coli (E. coli)562
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recording
IDImaging-IDAverage exposure time (sec.)Electron dose (e/Å2)Film or detector modelNum. of real images
118.3855.99FEI FALCON IV (4k x 4k)3881
217.2754.38FEI FALCON IV (4k x 4k)6441

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.6particle selection
2EPU3.5.1image acquisition
4cryoSPARC4.6CTF correction
7UCSF ChimeraX1.9.dev202410260116model fitting
9cryoSPARC4.6initial Euler assignment
10cryoSPARC4.6final Euler assignment
12cryoSPARC4.63D reconstruction3D Flex
13Coot0.9.8.93model refinement
Image processingDetails: Gain-corrected movies were aligned using cryoSPARC
CTF correctionDetails: CTF estimation and correction with cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34000 / Details: 3D Flexible refinement / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: L-P from 6U1X was rigid-body fitted in the map. N0-P from 3PMK (chains D and O) was rigid-body fitted in the map after deletion of the C-loop (aa 342-374). The model was then locally edited ...Details: L-P from 6U1X was rigid-body fitted in the map. N0-P from 3PMK (chains D and O) was rigid-body fitted in the map after deletion of the C-loop (aa 342-374). The model was then locally edited and refined to introduce mutations and solve clashes.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16U1X

6u1x

16U1X1PDBexperimental model
23PMK

3pmk

13PMK2PDBexperimental model

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