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- PDB-8ki6: Structure of tomato spotted wilt virus L protein binding to Ribavirin -

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Basic information

Entry
Database: PDB / ID: 8ki6
TitleStructure of tomato spotted wilt virus L protein binding to Ribavirin
ComponentsRNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN / tomato spotted wilt virus / L protein
Function / homology
Function and homology information


RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription
Similarity search - Function
RNA-directed RNA polymerase, tospovirus / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
Chem-RBV / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesOrthotospovirus tomatomaculae
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCao, L. / Wang, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: structure of tomato spotted wilt virus L protein
Authors: Cao, L. / Wang, X.
History
DepositionAug 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,7513
Polymers204,2631
Non-polymers4882
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 204262.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthotospovirus tomatomaculae
Production host: Spodoptera frugiperda multiple nucleopolyhedrovirus
References: UniProt: A0A7G8JUQ9, RNA-directed RNA polymerase
#2: Chemical ChemComp-RBV / 1-(beta-D-ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide / Ribavirin


Mass: 244.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12N4O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antivirus*YM
Has ligand of interestY

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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

ComponentName: Structure of tomato spotted wilt virus L protein binding to Ribavirin
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Orthotospovirus tomatomaculae
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 348921 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412988
ELECTRON MICROSCOPYf_angle_d0.98717499
ELECTRON MICROSCOPYf_dihedral_angle_d8.1971735
ELECTRON MICROSCOPYf_chiral_restr0.0531991
ELECTRON MICROSCOPYf_plane_restr0.0062186

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