5DRX

Crystal structure of the BCR Fab fragment from subset #4 case CLL240


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Distinct homotypic B-cell receptor interactions shape the outcome of chronic lymphocytic leukaemia.

Minici, C.Gounari, M.Ubelhart, R.Scarfo, L.Duhren-von Minden, M.Schneider, D.Tasdogan, A.Alkhatib, A.Agathangelidis, A.Ntoufa, S.Chiorazzi, N.Jumaa, H.Stamatopoulos, K.Ghia, P.Degano, M.

(2017) Nat Commun 8: 15746-15746

  • DOI: https://doi.org/10.1038/ncomms15746
  • Primary Citation of Related Structures:  
    5DRW, 5DRX, 5IFH

  • PubMed Abstract: 

    Cell-autonomous B-cell receptor (BcR)-mediated signalling is a hallmark feature of the neoplastic B lymphocytes in chronic lymphocytic leukaemia (CLL). Here we elucidate the structural basis of autonomous activation of CLL B cells, showing that BcR immunoglobulins initiate intracellular signalling through homotypic interactions between epitopes that are specific for each subgroup of patients with homogeneous clinicobiological profiles. The molecular details of the BcR-BcR interactions apparently dictate the clinical course of disease, with stronger affinities and longer half-lives in indolent cases, and weaker, short-lived contacts mediating the aggressive ones. The diversity of homotypic BcR contacts leading to cell-autonomous signalling reconciles the existence of a shared pathogenic mechanism with the biological and clinical heterogeneity of CLL and offers opportunities for innovative treatment strategies.


  • Organizational Affiliation

    Biocrystallography Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CLL240 heavy chain (VH and CH1 domains)A [auth H],
C [auth A]
228Homo sapiensMutation(s): 0 
Gene Names: IGHV4-34IGHJ6IGHG1*03
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CLL240 BCR light chainB [auth L],
D [auth B]
221Homo sapiensMutation(s): 0 
Gene Names: IGKV2-30IGKJ2IGKC*01
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.187α = 90
b = 92.327β = 90
c = 135.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
AIRCItaly5xMille
Fondazione Intesa San Paolo OnlusItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references