1NMA

N9 NEURAMINIDASE COMPLEXES WITH ANTIBODIES NC41 AND NC10: EMPIRICAL FREE-ENERGY CALCULATIONS CAPTURE SPECIFICITY TRENDS OBSERVED WITH MUTANT BINDING DATA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

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Literature

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: 7986-7997

  • DOI: 10.1021/bi00192a002
  • Primary Citation of Related Structures:  
    1NMA

  • PubMed Abstract: 
  • X-ray crystallographic coordinates of influenza virus N9 neuraminidase complexed with monoclonal antibodies NC41 and NC10 [Tulip et al. (1992) J. Mol. Biol. 227, 122-148] served as a starting point for calculations aimed at estimating free energy cha ...

    X-ray crystallographic coordinates of influenza virus N9 neuraminidase complexed with monoclonal antibodies NC41 and NC10 [Tulip et al. (1992) J. Mol. Biol. 227, 122-148] served as a starting point for calculations aimed at estimating free energy changes (delta G) of complex formation between the two antibodies and the neuraminidase. Using an empirical function incorporating hydrophobic, electrostatic, and conformational entropy effects, we estimated contributions individual neuraminidase residues make to complex formation (delta G(residue)) and compared the calculated values to experimentally measured differences in antibody binding between the wild-type and mutated neuraminidases [Nuss et al. (1993) Proteins 15, 121-132; calculations done without prior knowledge of the experimental data]. A good correspondence was found between the calculated delta G(residue) values and the mutant binding data in that side chains with large calculated delta G contributions (delta G(residue) < -1 kcal/mol) lie at sites of mutation which cause a marked reduction in antibody binding, and side chains for which delta G(residue) > -1 kcal/mol are sites at which a mutation does not have a marked effect on binding. Because most of the delta G(residue) < -1 kcal/mol side chains also make hydrogen bonds/salt bridges with the antibody, the correspondence of the effect of antibody binding with these electrostatic interactions (18 out of 27 for NC41 and, tentatively, 5 out of 7 for NC10) is about as good as that with predicted energetic residues. All the delta G(residue) < -1 kcal/mol neuraminidase side chains cluster around the most protruding surface regions and are thus spread over different epitope segments. Surprisingly, different residues were found to make the most critical contributions to the NC41 and NC10 complex stabilities despite the fact that the NC41 and NC10 antigenic epitopes overlap, having approximately 70% of surface residues in common. It is thus possible, for two different antibodies, to recognize the same protein surface in strikingly different ways. As only a fraction of the neuraminidase residues appear to make large contributions to antibody binding, the results also support the hypothesis of a "functional" epitope in antigen-antibody interactions. Positive trends between both backbone rigidity and residue accessibility in the complexed state, and contributions of these residues to binding, were also observed for the NC41 complex.


    Related Citations: 
    • Refined Crystal Structures of the Influenza Virus N9 Neuraminidase-Nc41 Fab Complex
      Tulip, W.R., Varghese, J.N., Laver, W.G., Webster, R.G., Colman, P.M.
      (1992) J Mol Biol 227: 122
    • 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 Structures 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 54: 257

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N9 NEURAMINIDASEN388Influenza A virusMutation(s): 0 
EC: 3.2.1.18
Find proteins for P05803 (Influenza A virus (strain A/Whale/Maine/1/1984 H13N9))
Explore P05803 
Go to UniProtKB:  P05803
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FAB NC10L109Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
FAB NC10H122Mus musculusMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
A
6 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
N
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.5α = 90
b = 171.5β = 90
c = 160.2γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Structure summary