1NN2

THREE-DIMENSIONAL STRUCTURE OF THE NEURAMINIDASE OF INFLUENZA VIRUS A(SLASH)TOKYO(SLASH)3(SLASH)67 AT 2.2 ANGSTROMS RESOLUTION

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report



Literature

Three-dimensional structure of the neuraminidase of influenza virus A/Tokyo/3/67 at 2.2 A resolution.

Varghese, J.N., Colman, P.M.

(1991) J Mol Biol 221: 473-486

  • DOI: 10.1016/0022-2836(91)80068-6
  • Primary Citation of Related Structures:  
    1NN2

  • PubMed Abstract: 

    • An atomic model of the tetrameric surface glycoprotein neuraminidase of influenza virus A/Tokyo/3/67 has been built and refined based on X-ray diffraction data at 2.2 A resolution. The crystallographic residual is 0.21 for data between 6 and 2.2 A re ...

    An atomic model of the tetrameric surface glycoprotein neuraminidase of influenza virus A/Tokyo/3/67 has been built and refined based on X-ray diffraction data at 2.2 A resolution. The crystallographic residual is 0.21 for data between 6 and 2.2 A resolution and the r.m.s. deviations from ideal geometry are 0.02 A for bond lengths and 3.9 degrees for bond angles. The model includes amino acid residues 83 to 469, four oligosaccharide structures N-linked at asparagine residues 86, 146, 200 and 234, a single putative Ca2+ ion site, and 85 water molecules. One of the oligosaccharides participates in a novel crystal contact. The folding pattern is a beta-sheet propeller as described earlier and details of the intramolecular interactions between the six beta-sheets are presented. Strain-invariant residues are clustered around the propeller axis on the upper surface of the molecule where they line the wall of a cavity into which sialic has been observed to bind. Strain-variable residues implicated in binding to antibodies surround this site.

    Organizational Affiliation: 

    CSIRO Division of Biomolecular Engineering, Parkville, Victoria, Australia.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEURAMINIDASEA388Influenza A virus (A/Tokyo/3/1967(H2N2))Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
Find proteins for P06820 (Influenza A virus (strain A/Tokyo/3/1967 H2N2))
Explore P06820 
Go to UniProtKB:  P06820
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2 N-Glycosylation
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-4-O-sulfo-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
C
7 N-Glycosylation
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
6 N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
CA
Query on CA
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.210 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.6α = 90
b = 139.6β = 90
c = 191γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1992-07-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Structure summary