3A1G

High-Resolution Crystal Structure of RNA polymerase PB1-PB2 subunits from Influenza A Virus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation 3D Report Full Report


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


Literature

Structural insight into the essential PB1-PB2 subunit contact of the influenza virus RNA polymerase

Sugiyama, K., Obayashi, E., Kawaguchi, A., Suzuki, Y., Tame, J.R.H., Nagata, K., Park, S.-Y.

(2009) EMBO J 28: 1803-1811

  • DOI: 10.1038/emboj.2009.138
  • Primary Citation of Related Structures:  
    2ZTT, 3A1G

  • PubMed Abstract: 

    • Influenza virus RNA-dependent RNA polymerase is a multi-functional heterotrimer, which uses a 'cap-snatching' mechanism to produce viral mRNA. Host cell mRNA is cleaved to yield a cap-bearing oligonucleotide, which can be extended using viral genomic ...

    Influenza virus RNA-dependent RNA polymerase is a multi-functional heterotrimer, which uses a 'cap-snatching' mechanism to produce viral mRNA. Host cell mRNA is cleaved to yield a cap-bearing oligonucleotide, which can be extended using viral genomic RNA as a template. The cap-binding and endonuclease activities are only activated once viral genomic RNA is bound. This requires signalling from the RNA-binding PB1 subunit to the cap-binding PB2 subunit, and the interface between these two subunits is essential for the polymerase activity. We have defined this interaction surface by protein crystallography and tested the effects of mutating contact residues on the function of the holo-enzyme. This novel interface is surprisingly small, yet, it has a crucial function in regulating the 250 kDa polymerase complex and is completely conserved among avian and human influenza viruses.

    Organizational Affiliation: 

    Protein Design Laboratory, Yokohama City University, Tsurumi, Yokohama, Japan.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase basic protein 2B, D40Influenza A virus (A/Puerto Rico/8/1934(H1N1))Mutation(s): 0 
Gene Names: PB2
Find proteins for P03428 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03428 
Go to UniProtKB:  P03428
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymerase catalytic subunitA, C80Influenza A virus (A/Puerto Rico/8/1934(H1N1))Mutation(s): 0 
Gene Names: PB1
EC: 2.7.7.48
Find proteins for P03431 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03431 
Go to UniProtKB:  P03431
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		B,DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.701α = 90
b = 69.987β = 97.94
c = 61.348γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance