5WOP

High Resolution Structure of Mutant CA09-PB2cap


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

High-resolution structure of the Influenza A virus PB2cap binding domain illuminates the changes induced by ligand binding.

Constantinides, A.Gumpper, R.Severin, C.Luo, M.

(2018) Acta Crystallogr F Struct Biol Commun 74: 122-127

  • DOI: 10.1107/S2053230X18000894

  • PubMed Abstract: 
  • In the face of increasing drug resistance and the rapidly increasing necessity for practicality in clinical settings, drugs targeting different viral proteins are needed in order to control influenza A and B. A small molecule that tenaciously adheres ...

    In the face of increasing drug resistance and the rapidly increasing necessity for practicality in clinical settings, drugs targeting different viral proteins are needed in order to control influenza A and B. A small molecule that tenaciously adheres to the PB2cap binding domain, part of the heterotrimeric RNA polymerase machinery of influenza A virus and influenza B virus, is a promising drug candidate. Understanding the anatomic behavior of PB2cap upon ligand binding will aid in the development of a more robust inhibitor. In this report, the anatomic behavior of the influenza A virus PB2cap domain is established by solving the crystal structure of native influenza A virus PB2cap at 1.52 Å resolution. By comparing it with the ligand-bound structure, the dissociation and rotation of the ligand-binding domain in PB2cap from the C-terminal domain is identified. This domain movement is present in many PB2cap structures, suggesting its functional relevance for polymerase activity.


    Related Citations: 
    • The cap-binding site of influenza virus protein PB2 as a drug target
      Severin, C.,Rocha de Moura, T.,Liu, Y.,Li, K.,Zheng, X.,Luo, M.
      (2016) Acta Crystallogr D Struct Biol 72: 245
    • Crystallization and X-ray crystallographic analysis of the cap-binding domain of influenza A virus H1N1 polymerase subunit PB2
      Liu, Y.,Meng, G.,Luo, M.,Zheng, X.
      (2013) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 69: 280


    Organizational Affiliation

    Department of Chemistry, Georgia State University, 50 Decatur Street, Atlanta, GA 30303, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase PB2
A, B
159Influenza A virusMutation(s): 0 
Gene Names: PB2
Find proteins for F4MEU3 (Influenza A virus)
Go to UniProtKB:  F4MEU3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.148 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 36.863α = 90.00
b = 72.429β = 103.18
c = 61.316γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-03-14
    Type: Database references