1FRG

CRYSTAL STRUCTURE, SEQUENCE, AND EPITOPE MAPPING OF A PEPTIDE COMPLEX OF AN ANTI-INFLUENZA HA PEPTIDE ANTIBODY FAB 26(SLASH)9: FINE-TUNING ANTIBODY SPECIFICITY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a peptide complex of anti-influenza peptide antibody Fab 26/9. Comparison of two different antibodies bound to the same peptide antigen.

Churchill, M.E.Stura, E.A.Pinilla, C.Appel, J.R.Houghten, R.A.Kono, D.H.Balderas, R.S.Fieser, G.G.Schulze-Gahmen, U.Wilson, I.A.

(1994) J.Mol.Biol. 241: 534-556

  • DOI: 10.1006/jmbi.1994.1530

  • PubMed Abstract: 
  • The three-dimensional structure of the complex of a second anti-peptide antibody (Fab 26/9) that recognizes the same six-residue epitope of an immunogenic peptide from influenza virus hemagglutinin (HA1; 75-110) as Fab 17/9 with the peptide has been ...

    The three-dimensional structure of the complex of a second anti-peptide antibody (Fab 26/9) that recognizes the same six-residue epitope of an immunogenic peptide from influenza virus hemagglutinin (HA1; 75-110) as Fab 17/9 with the peptide has been determined at 2.8 A resolution. The amino acid sequence of the variable region of the 26/9 antibody differs in 24 positions from that of 17/9, the first antibody in this series for which several ligand-bound and free structures have been determined and refined. Comparison of the 26/9-peptide with the 17/9-peptide complex structures shows that the two Fabs are very similar (r.m.s.d. 0.5 to 0.8 A) and that the peptide antigen (101-107) has virtually the same conformation (r.m.s.d. 0.3 to 0.8 A) when bound to both antibodies. A sequence difference in the 26/9 binding pocket (L94; His in 26/9, Asn in 17/9) results in an interaction with a bound water molecule that is not seen in the 17/9 structures. Epitope mapping shows that the relative specificity of 26/9 and 17/9 antibodies for individual positions of the peptide antigen are slightly different. Amino acid substitutions in the peptide, particularly at position SerP107, are tolerated to different extents by 17/9 and 26/9. Structural and sequence analysis suggests that amino acid differences near the peptide-binding site are responsible for altering slightly the specificity of 26/9 for three peptide residues and illustrates how amino acid substitutions can modify antibody-antigen interactions and thereby modulate antibody specificity.


    Related Citations: 
    • Structural Evidence for Induced Fit as a Mechanism for Antibody-Antigen Recognition
      Rini, J.M.,Schulze-Gahmen, U.,Wilson, I.A.
      (1992) Science 255: 959
    • Preliminary Crystallographic Data, Primary Sequence, and Binding Data for the Anti-Peptide Fab and its Complex with a Synthetic Peptide from Influenza Hemagglutinin
      Schulze-Gahmen, U.,Rini, J.M.,Arevalo, J.,Stura, E.A.,Kenten, J.H.,Wilson, I.A.
      (1988) J.Biol.Chem. 263: 17100
    • Detailed Analysis of the Free and Bound Conformations of an Antibody: X-Ray Structures of Fab 17(Slash)9 and Three Different Fab-Peptide Complexes
      Schulze-Gahmen, U.,Rini, J.M.,Wilson, I.A.
      (1993) J.Mol.Biol. 234: 1098


    Organizational Affiliation

    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG2A 26/9 FAB (LIGHT CHAIN)
L
217Mus musculusN/A
Find proteins for P01837 (Mus musculus)
Go to UniProtKB:  P01837
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG2A 26/9 FAB (HEAVY CHAIN)
H
220Mus musculusN/A
Find proteins for P01864 (Mus musculus)
Go to UniProtKB:  P01864
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 101 - 108)
P
10Influenza A virus (A/Assam/2112/2009(H3N2))Gene Names: HA
Find proteins for E3W6A8 (Influenza A virus (A/Assam/2112/2009(H3N2)))
Go to UniProtKB:  E3W6A8
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
P
NON-POLYMERH2 N

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ACE
Query on ACE
P
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.600α = 90.00
b = 115.100β = 90.00
c = 73.300γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-05-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-09-18
    Type: Source and taxonomy