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- PDB-9vs5: Structure of Ebinur lake virus polymerase at the elongation state -

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Basic information

Entry
Database: PDB / ID: 9vs5
TitleStructure of Ebinur lake virus polymerase at the elongation state
Components
  • RNA (5'-R(*GP*GP*AP*UP*AP*AP*AP*AP*AP*UP*AP*AP*U)-3')
  • RNA (5'-R(*GP*UP*AP*UP*AP*UP*CP*UP*CP*CP*AP*UP*UP*AP*UP*UP*UP*UP*UP*AP*UP*CP*C)-3')
  • RNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN/RNA / Viral protein / polymerase / elongation complex / L protein / RNA / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


host cell / RNA-directed RNA polymerase / nucleotide binding / viral RNA genome replication / hydrolase activity / RNA-directed RNA polymerase activity / DNA-templated transcription / metal ion binding
Similarity search - Function
: / Virus, RNA-directed RNA polymerase L, thumb ring domain / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / : / 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 / RNA (> 10) / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesEbinur lake virus
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsTang, J. / Deng, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis for RNA synthesis and inhibition of the orthobunyavirus polymerase
Authors: Tang, J. / Deng, Z.
History
DepositionJul 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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
P: RNA (5'-R(*GP*GP*AP*UP*AP*AP*AP*AP*AP*UP*AP*AP*U)-3')
T: RNA (5'-R(*GP*UP*AP*UP*AP*UP*CP*UP*CP*CP*AP*UP*UP*AP*UP*UP*UP*UP*UP*AP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)271,1013
Polymers271,1013
Non-polymers00
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: 259756.969 Da / Num. of mol.: 1 / Mutation: D79A,D92A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebinur lake virus / Gene: RdRp / Production host: Pichia (fungus)
References: UniProt: A0A059WLS9, RNA-directed RNA polymerase
#2: RNA chain RNA (5'-R(*GP*GP*AP*UP*AP*AP*AP*AP*AP*UP*AP*AP*U)-3')


Mass: 4197.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(*GP*UP*AP*UP*AP*UP*CP*UP*CP*CP*AP*UP*UP*AP*UP*UP*UP*UP*UP*AP*UP*CP*C)-3')


Mass: 7146.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestY
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

ComponentName: Structure of Ebinur lake virus polymerase elongation complex
Type: COMPLEX / Entity ID: #1, #3, #2 / Source: RECOMBINANT
Source (natural)Organism: Ebinur lake virus
Source (recombinant)Organism: Pichia (fungus)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 217551 / Symmetry type: POINT
RefinementHighest resolution: 3.31 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317194
ELECTRON MICROSCOPYf_angle_d0.71823341
ELECTRON MICROSCOPYf_dihedral_angle_d7.1252430
ELECTRON MICROSCOPYf_chiral_restr0.0442673
ELECTRON MICROSCOPYf_plane_restr0.0052864

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