1NMB

THE STRUCTURE OF A COMPLEX BETWEEN THE NC10 ANTIBODY AND INFLUENZA VIRUS NEURAMINIDASE AND COMPARISON WITH THE OVERLAPPING BINDING SITE OF THE NC41 ANTIBODY


Experimental Data Snapshot

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

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This is version 2.0 of the entry. See complete history


Literature

The structure of a complex between the NC10 antibody and influenza virus neuraminidase and comparison with the overlapping binding site of the NC41 antibody

Malby, R.L.Tulip, W.R.Harley, V.R.McKimm-Breschkin, J.L.Laver, W.G.Webster, R.G.Colman, P.M.

(1994) Structure 2: 733-746

  • DOI: https://doi.org/10.1016/s0969-2126(00)00074-5
  • Primary Citation of Related Structures:  
    1NMB

  • PubMed Abstract: 

    While it is well known that different antibodies can be produced against a particular antigen, and even against a particular site on an antigen, up until now there have been no structural studies of cross-reacting antibodies of this type. One antibody-antigen complex whose structure is known is that of the influenza virus antigen, neuraminidase, in complex with the NC41 antibody. Another anti-neuraminidase antibody, NC10, binds to an overlapping site on the antigen. The structure of the complex formed by this antibody with neuraminidase is described here and compared with the NC41-containing complex. The crystal structure of the NC10 Fab-neuraminidase complex has been refined to a nominal resolution of 2.5A. Approximately 80% of the binding site of the NC10 antibody on neuraminidase overlaps with that of the NC41 antibody. The epitope residues of neuraminidase are often engaged in quite different interactions with the two antibodies. Although the NC10 and NC41 antibodies have identical amino acid sequences within the first complementarity determining region of their heavy chains, this is not the basis of the cross-reaction. The capacity of two different proteins to bind to the same target structure on a third protein need not be based on the existence of identical or homologous amino acid sequences within those proteins. As we have demonstrated, amino acid residues on the common target structure may be in quite different chemical environments, and may also adopt different conformations within two protein-protein complexes.


  • Organizational Affiliation

    Biomolecular Research Institute, Parkville, Victoria, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N9 NEURAMINIDASEA [auth N]470Influenza A virusMutation(s): 0 
EC: 3.2.1.18
UniProt
Find proteins for P05803 (Influenza A virus (strain A/Whale/Maine/1/1984 H13N9))
Explore P05803 
Go to UniProtKB:  P05803
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UniProt GroupP05803
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FAB NC10B [auth L]109Mus musculusMutation(s): 0 
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FAB NC10C [auth H]122Mus musculusMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranoseD [auth A]7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G46836GH
GlyCosmos:  G46836GH
GlyGen:  G46836GH
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth N],
F [auth N]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth N]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.4α = 90
b = 169.4β = 90
c = 156.9γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-09-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-02-12
    Changes: Advisory, Data collection, Database references, Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary