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 ...

    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.

    Related Citations: 
    • Three-Dimensional Structures of Influenza Virus Neuraminidase-Antibody Complexes
      Colman, P.M., Tulip, W.R., Varghese, J.N., Tulloch, P.A., Baker, A.T., Laver, W.G., Air, G.M., Webster, R.G.
      (1989) Philos Trans R Soc London,ser B 323: 511
    • Crystal Structure of Neuraminidase-Antibody Complexes
      Tulip, W.R., Varghese, J.N., Webster, R.G., Air, G.M., Laver, W.G., Colman, P.M.
      (1989) Cold Spring Harb Symp Quant Biol LIV: 257
    • N9 Neuraminidase Complexes with Antibodies Nc41 and Nc10: Empirical Free Energy Calculations Capture Specificity Trends Observed with Mutant Binding Data
      Tulip, W.R., Harley, V.R., Webster, R.G., Novotny, J.
      (1994) Biochemistry 33: 7986
    • Refined Crystal Structure of the Influenza Virus N9 Neuraminidase-Nc41 Complex
      Tulip, W.R., Varghese, J.N., Laver, W.G., Webster, R.G., Colman, P.M.
      (1992) J Mol Biol 227: 122
    Organizational Affiliation: 

    Biomolecular Research Institute, Parkville, Victoria, Australia.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence 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))
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Go to UniProtKB:  P05803
Entity Groups  
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UniProt GroupP05803
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FAB NC10B [auth L]109Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
FAB NC10C [auth H]122Mus musculusMutation(s): 0 
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Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D 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 Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G46836GH
GlyCosmos:  G46836GH
GlyGen:  G46836GH
Small Molecules
Ligands 2 Unique
IDChainsName / 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		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
G [auth N]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 
  • 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