1HIM

STRUCTURAL EVIDENCE FOR INDUCED FIT AS A MECHANISM FOR ANTIBODY-ANTIGEN RECOGNITION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural evidence for induced fit as a mechanism for antibody-antigen recognition.

Rini, J.M.Schulze-Gahmen, U.Wilson, I.A.

(1992) Science 255: 959-965

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The three-dimensional structure of a specific antibody (Fab 17/9) to a peptide immunogen from influenza virus hemagglutinin [HA1(75-110)] and two independent crystal complexes of this antibody with bound peptide (TyrP100-LeuP108) have been determined ...

    The three-dimensional structure of a specific antibody (Fab 17/9) to a peptide immunogen from influenza virus hemagglutinin [HA1(75-110)] and two independent crystal complexes of this antibody with bound peptide (TyrP100-LeuP108) have been determined by x-ray crystallographic techniques at 2.0 A, 2.9 A, and 3.1 A resolution, respectively. The nonapeptide antigen assumes a type I beta turn in the antibody combining site and interacts primarily with the Fab hypervariable loops L3, H2, and H3. Comparison of the bound and unbound Fab structures shows that a major rearrangement in the H3 loop accompanies antigen binding. This conformational change results in the creation of a binding pocket for the beta turn of the peptide, allowing TyrP105 to be accommodated. The conformation of the peptide bound to the antibody shows similarity to its cognate sequence in the HA1, suggesting a possible mechanism for the cross-reactivity of this Fab with monomeric hemagglutinin. The structures of the free and antigen bound antibodies demonstrate the flexibility of the antibody combining site and provide an example of induced fit as a mechanism for antibody-antigen recognition.


    Related Citations: 
    • Preliminary Crystallographic Data, Primary Sequence, and Binding Data for an Anti-Peptide Fab and its Complex with a Synthetic Peptide from Influenza Virus Hemagglutinin
      Schulze-Gahmen, U.,Rini, J.M.,Arevalo, J.,Stura, E.A.,Kenten, J.H.,Wilson, I.A.
      (1988) J.Biol.Chem. 263: 17100


    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-KAPPA 17/9 FAB (LIGHT CHAIN)
H, J
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG2A-KAPPA 17/9 FAB (HEAVY CHAIN)
L, M
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 100-108)
P
9Influenza A virusMutation(s): 0 
Gene Names: HA
Find proteins for I6SHA6 (Influenza A virus)
Go to UniProtKB:  I6SHA6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
INFLUENZA HEMAGGLUTININ HA1 (STRAIN X47) (RESIDUES 100-108)
R
10Influenza A virusMutation(s): 0 
Gene Names: HA
Find proteins for I6SHA6 (Influenza A virus)
Go to UniProtKB:  I6SHA6
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
P, R
NON-POLYMERH2 N

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.200 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 60.080α = 89.90
b = 67.070β = 101.80
c = 73.240γ = 96.50
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: 1994-01-31
    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: 2015-12-23
    Type: Database references, Structure summary