3WI1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.931 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1371/journal.pone.0082020
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase basic protein 2
A
174Influenza A virus (strain 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))
Go to UniProtKB:  P03428
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGT
Query on MGT

Download SDF File 
Download CCD File 
A
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
C11 H20 N5 O14 P3
BUJQMJUTTBGELS-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.931 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.175 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 107.672α = 90.00
b = 107.672β = 90.00
c = 138.302γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-18
    Type: Initial release