1NNA

THREE-DIMENSIONAL STRUCTURE OF INFLUENZA A N9 NEURAMINIDASE AND ITS COMPLEX WITH THE INHIBITOR 2-DEOXY 2,3-DEHYDRO-N-ACETYL NEURAMINIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Three-dimensional structure of influenza A N9 neuraminidase and its complex with the inhibitor 2-deoxy 2,3-dehydro-N-acetyl neuraminic acid.

Bossart-Whitaker, P.Carson, M.Babu, Y.S.Smith, C.D.Laver, W.G.Air, G.M.

(1993) J.Mol.Biol. 232: 1069-1083

  • DOI: 10.1006/jmbi.1993.1461
  • Primary Citation of Related Structures:  1NNB

  • PubMed Abstract: 
  • We present here the three-dimensional structure of neuraminidase (E.C. 3.2.1.18) from influenza virus A/Tern/Australia/G70c/75 (N9), determined by the method of multiple isomorphous replacement, and the structure of the neuraminidase complexed with a ...

    We present here the three-dimensional structure of neuraminidase (E.C. 3.2.1.18) from influenza virus A/Tern/Australia/G70c/75 (N9), determined by the method of multiple isomorphous replacement, and the structure of the neuraminidase complexed with an inhibitor, 2-deoxy-2,3-dehydro-N-acetyl neuraminic acid (DANA). Native and inhibitor complex crystals are isomorphous and belong to space group I432 with unit cell dimensions of 183.78 A. The native enzyme structure and the inhibitor complex structure have been refined at 2.5 A and 2.8 A resolution, respectively, with crystallographic R-factor values of 0.193 for the native enzyme, and 0.179 for the inhibitor complex. The current enzyme model includes 387 amino acid residues which comprise the asymmetric unit. The root-mean-square deviation from ideal values is 0.013 A for bond lengths and 1.6 degree for bond angles. The neuraminidase (NA), as proteolytically cleaved from the virus, retains full enzymatic and antigenic activity, and is a box-shaped tetramer with edge lengths of 90 A and a maximal depth of 60 A. The NA tetramers are composed of crystallographically equivalent monomers related by circular 4-fold symmetry. Each monomer folds into six antiparallel beta-sheets of four strands. The secondary structure composition is 50% beta-sheet. The remaining 50% of the residues form 24 strand-connecting loops or turns. One of the loops contains a small alpha-helix. The structure of the complex of NA with DANA, a transition state analog, has enabled us to identify and characterize the site of enzyme catalysis. The center of mass of bound inhibitor is 32 A from the 4-fold axis of the tetramer, lodged at the end of a shallow crater of diameter 16 A with a depth of 8 to 10 A. There are 12 amino acid residues that directly bind DANA, with a further six conserved amino acids lining the active site pocket. The neuraminidase inhibitor complex provides a three-dimensional model which will be used to further the understanding of enzymatic hydrolysis and aid the design of specific, antineuraminidase antiviral compounds.


    Related Citations: 
    • Refined Atomic Structures of N9 Subtype Influenza Virus Neuraminidase and Escape Mutants
      Tulip, W.R.,Varghese, J.N.,Baker, A.T.,Van Donkelaar, A.,Laver, W.G.,Webster, R.G.,Colman, P.M.
      (1991) J.Mol.Biol. 221: 487
    • Influenza Virus Neuraminidase with Hemagglutinin Activity
      Laver, W.G.,Colman, P.M.,Webster, R.G.,Hinshaw, V.S.
      (1984) Virology 137: 314
    • Transfer of the Hemagglutinin Activity of Influenza Virus Neuraminidase Subtype N9 Into an N2 Background
      Nuss, J.M.,Air, G.M.
      (1991) Virology 183: 496
    • Three-Dimensional Structure of Neuraminidase of Subtype N9 from an Avian Influenza Virus
      Baker, A.T.,Varghese, J.N.,Laver, W.G.,Air, G.M.,Colman, P.M.
      (1987) Proteins 2: 111
    • Three-Dimensional Structure of Influenza A(Slash)Tern(Slash)Australia(Slash)G70C(Slash)75 N9 Neuraminidase and its Complex with the Inhibitor 2-Deoxy-2,3-Dehydro N-Acetyl Neuraminic Acid
      Bossart-Whitaker, P.J.
      (1992) Thesis --: --
    • Gene and Protein Sequence of an Influenza Neuraminidase with Hemagglutinin Activity
      Air, G.M.,Ritchie, L.R.,Laver, W.G.,Colman, P.M.
      (1985) Virology 145: 117


    Organizational Affiliation

    Department of Microbiology, University of Alabama at Birmingham 35294.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEURAMINIDASE
A
387Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9)Gene Names: NA
EC: 3.2.1.18
Find proteins for P03472 (Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9))
Go to UniProtKB:  P03472
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.193 
  • Space Group: I 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 183.780α = 90.00
b = 183.780β = 90.00
c = 183.780γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-04-30
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other