P453H/I471T mutant of PB2 middle domain from influenza virus A/Puerto Rico/8/34(H1N1) with m7GTP

Experimental Data Snapshot

  • Resolution: 1.93 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

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Conformational Polymorphism of m7GTP in Crystal Structure of the PB2 Middle Domain from Human Influenza A Virus

Tsurumura, T.Qiu, H.Yoshida, T.Tsumori, Y.Hatakeyama, D.Kuzuhara, T.Tsuge, H.

(2013) PLoS One 8: e82020-e82020

  • DOI: https://doi.org/10.1371/journal.pone.0082020
  • Primary Citation of Related Structures:  
    3WI0, 3WI1

  • PubMed Abstract: 

    Influenza pandemics with human-to-human transmission of the virus are of great public concern. It is now recognized that a number of factors are necessary for human transmission and virulence, including several key mutations within the PB2 subunit of RNA-dependent RNA polymerase. The structure of the middle domain in PB2 has been revealed with or without m(7)GTP, thus the middle domain is considered to be novel target for structure-based drug design. Here we report the crystal structure of the middle domain of H1N1 PB2 with or without m(7)GTP at 1.9 Å and 2.0 Å resolution, respectively, which has two mutations (P453H, I471T) to increase electrostatic potential and solubility. Here we report the m(7)GTP has unique conformation differ from the reported structure. 7-methyl-guanine is fixed in the pocket, but particularly significant change is seen in ribose and triphosphate region: the buried 7-methyl-guanine indeed binds in the pocket forming by H357, F404, E361 and K376 but the triphosphate continues directly to the outer domain. The presented conformation of m(7)GTP may be a clue for the anti-influenza drug-design.

  • Organizational Affiliation

    Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase basic protein 2174Influenza A virus (A/Puerto Rico/8/1934(H1N1))Mutation(s): 2 
Gene Names: PB2
Find proteins for P03428 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03428 
Go to UniProtKB:  P03428
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03428
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MGT

Download Ideal Coordinates CCD File 
C11 H20 N5 O14 P3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.93 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.672α = 90
b = 107.672β = 90
c = 138.302γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description