8KAD

Crystal structure of an antibody light chain tetramer with 3D domain swapping


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


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Literature

Structural and thermodynamic insights into antibody light chain tetramer formation through 3D domain swapping.

Sakai, T.Mashima, T.Kobayashi, N.Ogata, H.Duan, L.Fujiki, R.Hengphasatporn, K.Uda, T.Shigeta, Y.Hifumi, E.Hirota, S.

(2023) Nat Commun 14: 7807-7807

  • DOI: https://doi.org/10.1038/s41467-023-43443-4
  • Primary Citation of Related Structures:  
    8KAD

  • PubMed Abstract: 

    Overexpression of antibody light chains in small plasma cell clones can lead to misfolding and aggregation. On the other hand, the formation of amyloid fibrils from antibody light chains is related to amyloidosis. Although aggregation of antibody light chain is an important issue, atomic-level structural examinations of antibody light chain aggregates are sparse. In this study, we present an antibody light chain that maintains an equilibrium between its monomeric and tetrameric states. According to data from X-ray crystallography, thermodynamic and kinetic measurements, as well as theoretical studies, this antibody light chain engages in 3D domain swapping within its variable region. Here, a pair of domain-swapped dimers creates a tetramer through hydrophobic interactions, facilitating the revelation of the domain-swapped structure. The negative cotton effect linked to the β-sheet structure, observed around 215 nm in the circular dichroism (CD) spectrum of the tetrameric variable region, is more pronounced than that of the monomer. This suggests that the monomer contains less β-sheet structures and exhibits greater flexibility than the tetramer in solution. These findings not only clarify the domain-swapped structure of the antibody light chain but also contribute to controlling antibody quality and advancing the development of future molecular recognition agents and drugs.


  • Organizational Affiliation

    Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody light chain
A, B
120Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.255 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.78α = 90
b = 52.78β = 90
c = 260.29γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP26288080

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release