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- PDB-9h1y: Structure of the borna disease virus 1 replication full-length co... -

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Basic information

Entry
Database: PDB / ID: 9h1y
TitleStructure of the borna disease virus 1 replication full-length complex - reaction complex
Components
  • Phosphoprotein
  • RNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN / polymerase / phosphoprotein / bornavirus / RdRp
Function / homology
Function and homology information


exit of virus from host cell nucleus through nuclear pore / virion component / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / 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: 3.07 Å
AuthorsKeown, J.R. / Carrique, L. / Grimes, J.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust200835/Z/16/Z United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: The structure of the mammalian bornavirus polymerase complex.
Authors: Loïc Carrique / Franziska Günl / Adrian Deng / Jonathan M Grimes / Jeremy R Keown /
Abstract: Borna disease virus 1 (BoDV-1) is a non-segmented RNA virus with one of the smallest known RNA virus genomes. BoDV-1 replicates in the nucleus of infected cells using a virally encoded polymerase ...Borna disease virus 1 (BoDV-1) is a non-segmented RNA virus with one of the smallest known RNA virus genomes. BoDV-1 replicates in the nucleus of infected cells using a virally encoded polymerase complex composed of the large protein and phosphoprotein. Here, we present the BoDV-1 polymerase complex at resolutions up to 2.8 Å, describing the fully ordered large polymerase protein bound to tetrameric phosphoprotein. The complex is maintained through the ordered C-terminal region of one copy of the phosphoprotein. Analysis of the model reveals a conserved methyltransferase domain, though key S-adenosyl methionine binding residues are missing. While no RNA is observed in our models, analysis of a sample under reaction conditions induces an opening and closing of the template entry and exit channels, respectively. Higher-order polymerase assemblies suggest oligomerisation as a conserved feature of negative strand RNA virus polymerases. We provide a molecular framework to investigate bornavirus replication and transcription.
History
DepositionOct 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
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Revision 1.0Aug 20, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: Phosphoprotein
C: Phosphoprotein
D: Phosphoprotein
E: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,5467
Polymers295,4155
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: 196999.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borna disease virus 1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P52639, RNA-directed RNA polymerase
#2: Protein
Phosphoprotein / P protein / p23 / p24


Mass: 24603.912 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 frugiperda (fall armyworm) / References: UniProt: P0C799
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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: BoDV-1 Replication complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Borna disease virus 1
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMhepesHEPES1
2250 mMsodium chlorideNaCl1
30.5 mMdithiothreitolDTT1
45 % w/vglycerolGlycerol1
SpecimenConc.: 0.33 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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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: 2600 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 2.0rc1_5617 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106976 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 187.99 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003614333
ELECTRON MICROSCOPYf_angle_d0.508419435
ELECTRON MICROSCOPYf_chiral_restr0.03752250
ELECTRON MICROSCOPYf_plane_restr0.00362443
ELECTRON MICROSCOPYf_dihedral_angle_d3.9861935

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