9N0Q | pdb_00009n0q

3.09A Bornavirus L-P complex (without incubation with RNA/NTP) (state 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural insights into the dynamic mechanism of bornavirus polymerase.

Yang, G.Wang, D.Liu, B.

(2025) Proc Natl Acad Sci U S A 122: e2504779122-e2504779122

  • DOI: https://doi.org/10.1073/pnas.2504779122
  • Primary Citation Related Structures: 
    9N0Q, 9N0R, 9N0S, 9N0T, 9N0U

  • PubMed Abstract: 

    Borna disease virus 1 (BoDV-1), an emerging zoonotic pathogen from the Bornaviridae family, is neurotropic and can infect a variety of mammalian hosts, including humans. Linked to severe encephalitis and high mortality, BoDV-1 currently lacks licensed treatments or vaccines. The BoDV-1 polymerase complex, comprising the large (L) and phosphoprotein (P) subunits, is crucial for viral replication and transcription, making it a promising target for antiviral intervention. Here, we present the cryoelectron microscopy structure of the apo BoDV-1 L-P complex, revealing a unique "mitten-shaped" architecture. The structure characterizes key domains involved in RNA synthesis, including RNA-dependent RNA polymerase, polyribonucleotidyltransferase, and an inactive methyltransferase domain. While no RNA or NTPs were visible, we observed distinct conformational states, showing large-scale rearrangements of the P tetramer and L domains, as well as remodeling of the RNA template, nucleoside triphosphates, and nascent RNA entrances and/or exits, upon introducing RNA and NTPs. These findings highlight the dynamic structural changes probably associated with polymerase activity and advance the understanding of the BoDV-1 polymerase mechanisms, offering a basis for developing targeted antiviral strategies against this deadly pathogen.


  • Organizational Affiliation
    • Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912.

Macromolecule Content 

  • Total Structure Weight: 281.86 kDa 
  • Atom Count: 14,668 
  • Modeled Residue Count: 1,861 
  • Deposited Residue Count: 2,515 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase1,711OrthobornavirusMutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for P52639 (Borna disease virus (strain V))
Explore P52639 
Go to UniProtKB:  P52639
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52639
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
P protein
B, C, D, E
201OrthobornavirusMutation(s): 0 
UniProt
Find proteins for P0C799 (Borna disease virus (strain V))
Explore P0C799 
Go to UniProtKB:  P0C799
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C799
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207:
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2025-10-08
    Changes: Data collection, Database references
  • Version 1.2: 2025-10-15
    Changes: Data collection, Database references