2Q06

Crystal structure of Influenza A Virus H5N1 Nucleoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 

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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
  • Primary Citation of Related Structures:  
    2Q06

  • 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 important structural and functional role and represents an attractive drug target ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NucleoproteinA, B504Influenza A virusMutation(s): 0 
UniProt
Find proteins for Q9PX50 (Influenza A virus)
Explore Q9PX50 
Go to UniProtKB:  Q9PX50
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9PX50
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.578α = 90
b = 153.578β = 90
c = 153.578γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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