1HGE

BINDING OF INFLUENZA VIRUS HEMAGGLUTININ TO ANALOGS OF ITS CELL-SURFACE RECEPTOR, SIALIC ACID: ANALYSIS BY PROTON NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY AND X-RAY CRYSTALLOGRAPHY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Binding of influenza virus hemagglutinin to analogs of its cell-surface receptor, sialic acid: analysis by proton nuclear magnetic resonance spectroscopy and X-ray crystallography.

Sauter, N.K.Hanson, J.E.Glick, G.D.Brown, J.H.Crowther, R.L.Park, S.J.Skehel, J.J.Wiley, D.C.

(1992) Biochemistry 31: 9609-9621

  • Primary Citation of Related Structures:  1HGD, 1HGF, 1HGG, 1HGH, 1HGI, 1HGJ

  • PubMed Abstract: 
  • The interaction between influenza virus hemagglutinin and its cell-surface receptor, 5-N-acetylneuraminic acid (sialic acid), was probed by the synthesis of 12 sialic acid analogs, including derivatives at the 2-carboxylate, 5-acetamido, 4-, 7-, and ...

    The interaction between influenza virus hemagglutinin and its cell-surface receptor, 5-N-acetylneuraminic acid (sialic acid), was probed by the synthesis of 12 sialic acid analogs, including derivatives at the 2-carboxylate, 5-acetamido, 4-, 7-, and 9-hydroxyl, and glycosidic positions. The equilibrium dissociation constants of these analogs were determined by nuclear magnetic resonance spectroscopy. Ligand modifications that reduced or abolished binding included the replacement of the 2-carboxylate with a carboxamide, the substitution of azido or N-benzyloxycarbonyl groups for the 5-acetamido group, and the replacement of the 9-hydroxyl with amino or O-acetyl moieties. Modifications having little effect on binding included the introduction of longer chains at the 4-hydroxyl position, the replacement of the acetamido methyl group with an ethyl group, and the removal of the 7-hydroxyl group. X-ray diffraction studies yielded 3 A resolution crystal structures of hemagglutinin in complex with four of the synthetic analogs [alpha-2-O-methyl-, 4-O-acetyl-alpha-2-O-methyl-, 9-amino-9-deoxy-alpha-2-O-methyl-, and alpha-2-O-(4'-benzylamidocarboxybutyl)-N-acetylneuraminic acid] and with the naturally occurring cell-surface saccharide (alpha 2-3)sialyllactose. The X-ray studies unambiguously establish the position and orientation of bound sialic acid, indicate the position of the lactose group of (alpha 2-3)sialyllactose, and suggest the location of an alpha-glycosidic chain (4'-benzylamidocarboxybutyl) that increases the binding affinity of sialic acid by a factor of about 3. Although the protein complexed with alpha-2-O-methylsialic acid contains the mutation Gly-135-->Arg near the ligand binding site, the mutation apparently does not affect the ligand's position. The X-ray studies allow us to interpret the binding affinities in terms of the crystallographic structure. The results suggest further experiments which could lead to the design of tight binding inhibitors of possible therapeutic value.


    Related Citations: 
    • The Structure of a Membrane Fusion Mutant of the Influenza Virus Hemagglutinin
      Weis, W.I.,Cusack, S.C.,Brown, J.H.,Daniels, R.S.,Skehel, J.J.,Wiley, D.C.
      (1990) Embo J. 9: 17
    • Structural Identification of the Antibody-Binding Sites of Hong Kong Influenza Hemagglutinin and Their Involvement in Antigenic Variation
      Wiley, D.C.,Wilson, I.A.,Skehel, J.J.
      (1981) Nature 289: 373
    • Three-Dimensional Structure of an Antigenic Mutant of the Influenza Virus Hemagglutinin
      Knossow, M.,Daniels, R.S.,Douglas, A.R.,Skehel, J.J.,Wiley, D.C.
      (1984) Nature 311: 678
    • Structure of the Hemagglutinin Membrane Glycoprotein of Influenza Virus at 3 Angstroms Resolution
      Wilson, I.A.,Skehel, J.J.,Wiley, D.C.
      (1981) Nature 289: 366
    • Crystallographic Detection of a Second Ligand Binding Site in Influenza Virus Hemagglutinin
      Sauter, N.K.,Glick, G.D.,Crowther, R.L.,Park, S.-J.,Eisen, M.B.,Skehel, J.J.,Knowles, J.R.,Wiley, D.C.
      (1992) Proc.Natl.Acad.Sci.USA 89: 324
    • The Refinement of the Hemagglutinin Membrane Glycoprotein of Influenza Virus
      Knossow, M.,Lewis, M.,Rees, D.,Wilson, I.A.,Skehel, J.J.,Wiley, D.C.
      (1986) Acta Crystallogr.,Sect.B 42: 627
    • Refinement of the Influenza Virus Hemagglutinin by Simulated Annealing
      Weis, W.I.,Brunger, A.T.,Skehel, J.J.,Wiley, D.C.
      (1990) J.Mol.Biol. 212: 737
    • Structure of the Influenza Virus Hemagglutinin Complexed with its Receptor, Sialic Acid
      Weis, W.I.,Brown, J.H.,Cusack, S.,Paulson, J.C.,Skehel, J.J.,Wiley, D.C.
      (1988) Nature 333: 426
    • Crystallization and X-Ray Diffraction Studies on the Hemagglutinin Glycoprotein from the Membrane of Influenza Virus
      Wiley, D.C.,Skehel, J.J.
      (1977) J.Mol.Biol. 112: 343


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, Cambridge, Massachusetts.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMAGGLUTININ, (G135R), HA1 CHAIN
A, C, E
328Influenza A virus (strain A/X-31 H3N2)Gene Names: HA
Find proteins for P03438 (Influenza A virus (strain A/X-31 H3N2))
Go to UniProtKB:  P03438
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HEMAGGLUTININ, (G135R), HA1 CHAIN
B, D, F
175Influenza A virus (strain A/X-31 H3N2)Gene Names: HA
Find proteins for P03438 (Influenza A virus (strain A/X-31 H3N2))
Go to UniProtKB:  P03438
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, C, E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MNA
Query on MNA

Download SDF File 
Download CCD File 
A, C, E
2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID
C12 H21 N O9
NJRVVFURCKKXOD-MIDKXNQYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MNAKd: 5400000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Work: 0.225 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 163.100α = 90.00
b = 163.100β = 90.00
c = 176.900γ = 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: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance