Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.92 kDa 
• Atom Count: 3431 
• Residue Count: 442 
• Unique protein chains: 3

2A6I

Crystal structure analysis of the anti-arsonate germline antibody 36-65 in complex with a phage display derived dodecapeptide KLASIPTHTSPL

• DOI: 10.2210/pdb2A6I/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2005-07-02 Released: 2006-06-13 
• Deposition Author(s): Sethi, D.K., Agarwal, A., Manivel, V., Rao, K.V., Salunke, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.264 
• R-Value Work: 0.245 
• R-Value Observed: 0.246 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5VGA

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

• PubMed: 16618601 
• DOI: 10.1016/j.immuni.2006.02.010
• Primary Citation of Related Structures:  
  2A6D, 2A6K, 2A6J, 2A6I


• 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 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.

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Organizational Affiliation: 

National Institute of Immunology, New Delhi 110067, India.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Germline antibody 36-65 Fab light chain	A	214	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Germline antibody 36-65 Fab heavy chain	B	222	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Dodecapeptide: KLASIPTHTSPL	P	12	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.264 
• R-Value Work: 0.245 
• R-Value Observed: 0.246 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.182	α = 90
b = 76.971	β = 101.97
c = 59.122	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
AUTOMAR	data reduction
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-07-02 
• Released Date: 2006-06-13 
Deposition Author(s): Sethi, D.K., Agarwal, A., Manivel, V., Rao, K.V., Salunke, D.M.

Revision History 

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