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- PDB-9q3a: Structure of the Borna Disease Virus 1 L and co-factor P Protein ... -

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Basic information

Entry
Database: PDB / ID: 9q3a
TitleStructure of the Borna Disease Virus 1 L and co-factor P Protein in an apo state
Components
  • Isoform p24 of Phosphoprotein
  • RNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN / TRANSFERASE / L Protein / Polymerase / NNS / Phosphoprotein
Function / homology
Function and homology information


: / virion component / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / symbiont-mediated suppression of host innate immune response / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / host cell nucleus / ATP binding
Similarity search - Function
Borna disease virus P24 / Borna disease virus P24 protein / 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.
Similarity search - Domain/homology
Phosphoprotein / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesBorna disease virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsOgino, T. / Chakrapani, S. / Gibbs, E. / Ogino, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI176323 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI146172 United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structure and function of the RNA polymerase complex of Borna disease virus, a nuclear-replicating non-segmented negative-strand RNA virus.
Authors: Eric Gibbs / Minako Ogino / Takehiro Kanda / Dean Watkins / Kyle Whiddon / Keizo Tomonaga / Sudha Chakrapani / Tomoaki Ogino /
Abstract: Borna disease virus 1 (BoDV-1) is a non-segmented negative-strand (NNS) RNA virus that uniquely replicates in the nucleus of mammalian host cells, in contrast to most NNS RNA viruses that replicate ...Borna disease virus 1 (BoDV-1) is a non-segmented negative-strand (NNS) RNA virus that uniquely replicates in the nucleus of mammalian host cells, in contrast to most NNS RNA viruses that replicate in the cytoplasm. The mechanisms underlying nuclear replication of BoDV-1 and related bornaviruses with their RNA-dependent RNA polymerase (RdRp) complexes remain poorly understood. Here, we report the 2.8 Å cryo-EM structure of the BoDV-1 RdRp complex, comprising the large (L) protein and tetrameric phosphoprotein (P). The L protein features an N-terminal superdomain containing the RdRp and GDP polyribonucleotidyltransferase (PRNTase, mRNA-capping enzyme) domains, along with three C-terminal appendages, including a methyltransferase-like domain. The RdRp initiates de novo RNA synthesis internally at the genomic promoter, producing 5'-triphosphorylated transcripts corresponding to the 5' end of the anti-genome. P interacts with the fingers RdRp subdomain of L. Structure-guided mutagenesis shows that the residues involved in the L-P interaction are essential for efficient transcription initiation and, consequently, for viral gene expression. A flexible loop within the PRNTase domain, analogous to the rhabdovirus priming-capping loop, appears critical for transcription initiation. These findings provide the structural and functional insights into the BoDV-1 RdRp and support a shared evolutionary origin between nuclear and cytoplasmic NNS RNA viruses.
History
DepositionAug 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 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
D: Isoform p24 of Phosphoprotein
B: Isoform p24 of Phosphoprotein
C: Isoform p24 of Phosphoprotein
E: Isoform p24 of Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,1806
Polymers283,1145
Non-polymers651
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 / Protein L / Large structural protein / Replicase / Transcriptase


Mass: 193155.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borna disease virus 1
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q8JMN0, RNA-directed RNA polymerase
#2: Protein
Isoform p24 of Phosphoprotein / P protein / p23 / p24


Mass: 22489.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borna disease virus 1 / Gene: P/X
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: P0C798
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Zn
Has ligand of interestN
Has protein modificationY

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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: Borna Disease Virus 1 L and co-factor P Protein / Type: COMPLEX / Entity ID: #2, #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Borna disease virus 1
Source (recombinant)Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 16000 nm / Nominal defocus min: 8000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
7Coot0.9.8.96model fitting
9cryoSPARC4.6.2initial Euler assignment
10RELION5final Euler assignment
12RELION53D reconstruction
13PHENIX1.21.2-5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224617 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model

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