8XKJ | pdb_00008xkj

Ckappa domain of human immunoglobulin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Identification of potential C1-binding sites in the immunoglobulin CL domains.

Yanaka, S.Kodama, A.Nishiguchi, S.Fujita, R.Shen, J.Boonsri, P.Sung, D.Isono, Y.Yagi, H.Miyanoiri, Y.Uchihashi, T.Kato, K.

(2024) Int Immunol 36: 405-412

  • DOI: https://doi.org/10.1093/intimm/dxae017
  • Primary Citation of Related Structures:  
    8XKJ, 8XKK, 8XLB, 8XLC

  • PubMed Abstract: 

    Immunoglobulin G (IgG) molecules that bind antigens on the membrane of target cells spontaneously form hexameric rings, thus recruiting C1 to initiate the complement pathway. However, our previous report indicated that a mouse IgG mutant lacking the Cγ1 domain activates the pathway independently of antigen presence through its monomeric interaction with C1q via the CL domain, as well as Fc. In this study, we investigated the potential interaction between C1q and human CL isoforms. Quantitative single-molecule observations using high-speed atomic force microscopy revealed that human Cκ exhibited comparable C1q binding capabilities with its mouse counterpart, surpassing the Cλ types, which have a higher isoelectric point than the Cκ domains. Nuclear magnetic resonance and mutation experiments indicated that the human and mouse Cκ domains share a common primary binding site for C1q, centred on Glu194, a residue conserved in the Cκ domains but absent in the Cλ domains. Additionally, the Cγ1 domain, with its high isoelectric point, can cause electrostatic repulsion to the C1q head and impede the C1q-interaction adjustability of the Cκ domain in Fab. The removal of the Cγ1 domain is considered to eliminate these factors and thus promote Cκ interaction with C1q with the potential risk of uncontrolled activation of the complement pathway in vivo in the absence of antigen. However, this research underscores the presence of potential subsites in Fab for C1q binding, offering promising targets for antibody engineering to refine therapeutic antibody design.


  • Organizational Affiliation
    • Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoglobulin kappa light chain111Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX7 (Homo sapiens)
Explore P0DOX7 
Go to UniProtKB:  P0DOX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOX7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 40 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanJP22H02755
Japan Agency for Medical Research and Development (AMED)JapanJP21ae0121020h0001
Japan Agency for Medical Research and Development (AMED)JapanJP21ae0121013h0301

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release