2A6K

Crystal Structure Analysis of the germline antibody 36-65 Fab in complex with the dodecapeptide SLGDNLTNHNLR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Differential epitope positioning within the germline antibody paratope enhances promiscuity in the primary immune response.

Sethi, D.K.Agarwal, A.Manivel, V.Rao, K.V.Salunke, D.M.

(2006) Immunity 24: 429-438

  • DOI: 10.1016/j.immuni.2006.02.010
  • Primary Citation of Related Structures:  
  • Also Cited By: 5VGA

  • PubMed Abstract: 
  • Correlation between the promiscuity of the primary antibody response and conformational flexibility in a germline antibody was addressed by using germline antibody 36-65. Crystallographic analyses of the 36-65 Fab with three independent dodecapeptide ...

    Correlation between the promiscuity of the primary antibody response and conformational flexibility in a germline antibody was addressed by using germline antibody 36-65. Crystallographic analyses of the 36-65 Fab with three independent dodecapeptides provided mechanistic insights into the generation of antibody diversity. While four antigen-free Fab molecules provided a quantitative description of the conformational repertoire of the antibody CDRs, three Fab molecules bound to structurally diverse peptide epitopes exhibited a common paratope conformation. Each peptide revealed spatially different footprints within the antigen-combining site. However, a conformation-specific lock involving two shared residues, which were also associated with hapten binding, was discernible. Unlike the hapten, the peptides interacted with residues that undergo somatic mutations, suggesting a possible mechanism for excluding "nonspecific" antigens during affinity maturation. The observed multiple binding modes of diverse epitopes within a common paratope conformation of a germline antibody reveal a simple, yet elegant, mechanism for expanding the primary antibody repertoire.


    Organizational Affiliation

    National Institute of Immunology, New Delhi 110067, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Germline antibody 36-65 Fab light chain
A, L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Germline antibody 36-65 Fab heavy chain
B, H
222Mus musculusMutation(s): 0 
Gene Names: Igh
Find proteins for Q6PF95 (Mus musculus)
Go to UniProtKB:  Q6PF95
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DODECAPEPTIDE: SLGDNLTNHNLR
P
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.245 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.135α = 90.00
b = 144.920β = 104.35
c = 70.991γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
AMoREphasing
AUTOMARdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description
  • Version 1.4: 2018-03-21
    Type: Database references