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- PDB-8kia: Tomato spotted wilt virus L protein (apo state) -

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Basic information

Entry
Database: PDB / ID: 8kia
TitleTomato spotted wilt virus L protein (apo state)
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
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesOrthotospovirus tomatomaculae
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 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


Theoretical massNumber of molelcules
Total (without water)204,3941
Polymers204,3941
Non-polymers00
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 / Large structural protein / Replicase / Transcriptase


Mass: 204394.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthotospovirus tomatomaculae / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A0A7G8JUQ9, RNA-directed RNA polymerase

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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: Tomato spotted wilt virus Lprotein / Type: COMPLEX / Entity ID: all / 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: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 359068 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00612952
ELECTRON MICROSCOPYf_angle_d1.30117447
ELECTRON MICROSCOPYf_dihedral_angle_d7.0151693
ELECTRON MICROSCOPYf_chiral_restr0.0631983
ELECTRON MICROSCOPYf_plane_restr0.0072182

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