3CM8

A RNA polymerase subunit structure from virus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.899 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Crystal structure of the polymerase PAC-PB1N complex from an avian influenza H5N1 virus

He, X., Zhou, J., Bartlam, M., Zhang, R., Ma, J., Lou, Z., Li, X., Li, J., Joachimiak, A., Zeng, Z., Ge, R., Rao, Z., Liu, Y.

(2008) Nature 454: 1123-1126

  • DOI: 10.1038/nature07120

  • PubMed Abstract: 

    • The recent emergence of highly pathogenic avian influenza A virus strains with subtype H5N1 pose a global threat to human health. Elucidation of the underlying mechanisms of viral replication is critical for development of anti-influenza virus drugs. ...

    The recent emergence of highly pathogenic avian influenza A virus strains with subtype H5N1 pose a global threat to human health. Elucidation of the underlying mechanisms of viral replication is critical for development of anti-influenza virus drugs. The influenza RNA-dependent RNA polymerase (RdRp) heterotrimer has crucial roles in viral RNA replication and transcription. It contains three proteins: PA, PB1 and PB2. PB1 harbours polymerase and endonuclease activities and PB2 is responsible for cap binding; PA is implicated in RNA replication and proteolytic activity, although its function is less clearly defined. Here we report the 2.9 ångström structure of avian H5N1 influenza A virus PA (PA(C), residues 257-716) in complex with the PA-binding region of PB1 (PB1(N), residues 1-25). PA(C) has a fold resembling a dragon's head with PB1(N) clamped into its open 'jaws'. PB1(N) is a known inhibitor that blocks assembly of the polymerase heterotrimer and abolishes viral replication. Our structure provides details for the binding of PB1(N) to PA(C) at the atomic level, demonstrating a potential target for novel anti-influenza therapeutics. We also discuss a potential nucleotide binding site and the roles of some known residues involved in polymerase activity. Furthermore, to explore the role of PA in viral replication and transcription, we propose a model for the influenza RdRp heterotrimer by comparing PA(C) with the lambda3 reovirus polymerase structure, and docking the PA(C) structure into an available low resolution electron microscopy map.

    Organizational Affiliation: 

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase acidic protein
A
471Influenza A virusMutation(s): 0 
Gene Names: PA
EC: 3.1.-.-
Find proteins for Q9EA60 (Influenza A virus)
Go to UniProtKB:  Q9EA60
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide from RNA-directed RNA polymerase catalytic subunit
B
30Influenza A virus (strain A/Hong Kong/156/1997 H5N1 genotype Gs/Gd)Mutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
Find proteins for Q9WLS3 (Influenza A virus (strain A/Hong Kong/156/1997 H5N1 genotype Gs/Gd))
Go to UniProtKB:  Q9WLS3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.899 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.224 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 121.942α = 90.00
b = 121.942β = 90.00
c = 134.594γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PDB_EXTRACTdata extraction
SHARPphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance