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 Å
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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


  • 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: 
    • 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
    • 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
    • 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 Harbor Symp.Quant.Biol. 54: 257


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N9 NEURAMINIDASE
N
388Influenza A virus (strain A/Whale/Maine/1/1984 H13N9)Gene Names: NA
EC: 3.2.1.18
Find proteins for P05803 (Influenza A virus (strain A/Whale/Maine/1/1984 H13N9))
Go to UniProtKB:  P05803
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FAB NC10
L
109N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FAB NC10
H
122N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
N
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
N
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.200 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 171.500α = 90.00
b = 171.500β = 90.00
c = 160.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-09-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance