1NSB

THE 2.2 ANGSTROMS RESOLUTION CRYSTAL STRUCTURE OF INFLUENZA B NEURAMINIDASE AND ITS COMPLEX WITH SIALIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The 2.2 A resolution crystal structure of influenza B neuraminidase and its complex with sialic acid.

Burmeister, W.P.Ruigrok, R.W.Cusack, S.

(1992) EMBO J. 11: 49-56


  • PubMed Abstract: 
  • Influenza virus neuraminidase catalyses the cleavage of terminal sialic acid, the viral receptor, from carbohydrate chains on glycoproteins and glycolipids. We present the crystal structure of the enzymatically active head of influenza B virus neuram ...

    Influenza virus neuraminidase catalyses the cleavage of terminal sialic acid, the viral receptor, from carbohydrate chains on glycoproteins and glycolipids. We present the crystal structure of the enzymatically active head of influenza B virus neuraminidase from the strain B/Beijing/1/87. The native structure has been refined to a crystallographic R-factor of 14.8% at 2.2 A resolution and its complex with sialic acid refined at 2.8 A resolution. The overall fold of the molecule is very similar to the already known structure of neuraminidase from influenza A virus, with which there is amino acid sequence homology of approximately 30%. Two calcium binding sites have been identified. One of them, previously undescribed, is located between the active site and a large surface antigenic loop. The calcium ion is octahedrally co-ordinated by five oxygen atoms from the protein and one water molecule. Sequence comparisons suggest that this calcium site should occur in all influenza A and B virus neuraminidases. Soaking of sialic acid into the crystals has enabled the mode of binding of the reaction product in the putative active site pocket to be revealed. All the large side groups of the sialic acid are equatorial and are specifically recognized by nine fully conserved active site residues. These in turn are stabilized by a second shell of 10 highly conserved residues principally by an extensive network of hydrogen bonds.


    Related Citations: 
    • Sequence and Crystallization of Influenza Virus B(Slash)Beijing(Slash)1(Slash)87 Neuraminidase
      Burmeister, W.-P.,Daniels, R.S.,Dayan, S.,Gagnon, J.,Cusack, S.,Ruigrok, R.W.H.
      (1991) Virology 180: 266


    Organizational Affiliation

    EMBL Outstation, c/o ILL, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEURAMINIDASE
A, B
390Influenza B virus (strain B/Beijing/1/1987)Gene Names: NA
EC: 3.2.1.18
Find proteins for P27907 (Influenza B virus (strain B/Beijing/1/1987))
Go to UniProtKB:  P27907
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.148 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.900α = 90.00
b = 88.900β = 90.00
c = 222.800γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    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: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-11-29
    Type: Advisory, Derived calculations, Other