2Q06

Crystal structure of Influenza A Virus H5N1 Nucleoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the influenza virus A H5N1 nucleoprotein: implications for RNA binding, oligomerization, and vaccine design.

Ng, A.K.Zhang, H.Tan, K.Li, Z.Liu, J.H.Chan, P.K.Li, S.M.Chan, W.Y.Au, S.W.Joachimiak, A.Walz, T.Wang, J.H.Shaw, P.C.

(2008) Faseb J. 22: 3638-3647

  • DOI: 10.1096/fj.08-112110

  • PubMed Abstract: 
  • The threat of a pandemic outbreak of influenza virus A H5N1 has become a major concern worldwide. The nucleoprotein (NP) of the virus binds the RNA genome and acts as a key adaptor between the virus and the host cell. It, therefore, plays an importan ...

    The threat of a pandemic outbreak of influenza virus A H5N1 has become a major concern worldwide. The nucleoprotein (NP) of the virus binds the RNA genome and acts as a key adaptor between the virus and the host cell. It, therefore, plays an important structural and functional role and represents an attractive drug target. Here, we report the 3.3-A crystal structure of H5N1 NP, which is composed of a head domain, a body domain, and a tail loop. Our structure resolves the important linker segments (residues 397-401, 429-437) that connect the tail loop with the remainder of the molecule and a flexible, basic loop (residues 73-91) located in an arginine-rich groove surrounding Arg150. Using surface plasmon resonance, we found the basic loop and arginine-rich groove, but mostly a protruding element containing Arg174 and Arg175, to be important in RNA binding by NP. We also used our crystal structure to build a ring-shaped assembly of nine NP subunits to model the miniribonucleoprotein particle previously visualized by electron microscopy. Our study of H5N1 NP provides insight into the oligomerization interface and the RNA-binding groove, which are attractive drug targets, and it identifies the epitopes that might be used for universal vaccine development.


    Organizational Affiliation

    Department of Biochemistry and Center for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoprotein
A, B
504Influenza A virusMutation(s): 0 
Gene Names: NP
Find proteins for Q9PX50 (Influenza A virus)
Go to UniProtKB:  Q9PX50
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.202 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 153.578α = 90.00
b = 153.578β = 90.00
c = 153.578γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
MOLREPphasing
REFMACrefinement
SBC-Collectdata collection
PDB_EXTRACTdata extraction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Derived calculations, Refinement description, Version format compliance