9JKC | pdb_00009jkc

Crystal structure of Aspergillus fumigatus polymycovirus 1 ploymerase (residues 85-763) in its apo state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.206 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Literature

An evolutionarily unique viral RdRP suggests a common dual-function feature of the priming element.

Jia, H.Liu, S.Rao, G.Liu, Q.Wu, J.Cao, S.Gong, P.

(2025) Sci Adv 11: eadv9640-eadv9640

  • DOI: https://doi.org/10.1126/sciadv.adv9640
  • Primary Citation Related Structures: 
    9JKC, 9JKD

  • PubMed Abstract: 

    Many RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses use de novo initiation strategy to start RNA synthesis, and they usually contain a priming element (PE) to interact with template RNA and priming nucleoside triphosphate to facilitate initiation. Upon transition to elongation in dengue virus 2 (DENV2) RdRP, PE refolds and contributes to elongation complex stability by interacting with the upstream RNA duplex. However, whether this PE dual-function feature commonly exists in viral RdRPs remains elusive, as PE is highly diverse among the entire RNA virus group. Here, a more complexed PE refolding is observed in RdRP crystal structures of Aspergillus fumigatus polymycovirus-1 (AfuPmV-1), a polymycovirus evolutionarily connecting positive-strand and double-stranded RNA viruses. Although structural details and enzymology features are very different in transition from initiation to elongation in DENV2 and AfuPmV-1 RdRPs, what is in common is the PE dual-function feature that demonstrates functional conservation beyond sequence and structure.


  • Organizational Affiliation
    • State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China.

Macromolecule Content 

  • Total Structure Weight: 384.57 kDa 
  • Atom Count: 25,293 
  • Modeled Residue Count: 3,292 
  • Deposited Residue Count: 3,450 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA dependent RNA polymerase
A, B, C, D, E
690Aspergillus fumigatus tetramycovirus 1Mutation(s): 0 
Gene Names: RdRP
UniProt
Find proteins for A0A0H5BRR0 (Aspergillus fumigatus tetramycovirus 1)
Explore A0A0H5BRR0 
Go to UniProtKB:  A0A0H5BRR0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H5BRR0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.206 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 257.961α = 90
b = 182.916β = 103.79
c = 118.681γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2018YFA0507200
National Natural Science Foundation of China (NSFC)China32300139

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Database references