9GFF | pdb_00009gff

BCR Fab from the subset 1 chronic lymphocytic leukaemia case P10015

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-08-09 Released: 2025-08-20 
  • Deposition Author(s): Minici, C., Degano, M.
  • Funding Organization(s): Italian Association for Cancer Research, Worldwide Cancer Research, Italian Ministry of Health

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.235 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Defective cell-autonomous signalling and antigenic polyreactivity of B-cell receptors from chronic lymphocytic leukaemia stereotyped subset 1.

Cocomazzi, P.G.Iatrou, A.Minici, C.Gounari, M.Linder, A.T.Akpinaroglu, C.Patrone, M.Broggini, L.Frenquelli, M.Sarrigeorgiou, I.Lymberi, P.Petrakis, G.Koletsa, T.Scarfo, L.Agathangelidis, A.Jumaa, H.Maity, P.C.Ghia, P.Stamatopoulos, K.Degano, M.

(2025) Nat Commun 17: 1280-1280

  • DOI: https://doi.org/10.1038/s41467-025-68040-5
  • Primary Citation Related Structures: 
    9GFF, 9GFG, 9GFH

  • PubMed Abstract: 

    A shared feature of B-cell receptors (BCRs) expressed on neoplastic B cells from patients with chronic lymphocytic leukaemia (CLL) concerns their continual activation of intracellular signalling without requiring external antigens. This autonomous signalling mechanism has previously been demonstrated to arise from BCR-BCR homotypic interactions in three distinct stereotyped CLL subsets (2, 4 and 169). CLL subset 1 is the second largest stereotyped subset, epitomizing unmutated CLL and known for a particularly aggressive clinical course. Here we show that, despite their significant sequence similarity, BCRs originating from three different subset 1 CLL cases exhibit variations in their combining site structures and associated physicochemical properties. Subset 1 BCRs are characterized by a common reactivity pattern towards various autoantigens, though they maintain distinct receptor-specific characteristics. Analysis of crystal structures of the respective BCR Fab fragments reveals lack of conservation in intermolecular crystal contacts, paralleled by no self-association in solution and incapacity to induce intracellular signalling when expressed in a model B-cell line. These findings suggest that cell-autonomous signalling may not be universally present across all CLL, implying the existence of other mechanisms in sustaining leukemic cell proliferation and CLL progression mediated by BCR signalling.


  • Organizational Affiliation
    • Biocrystallography Unit, Department of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, 20132, Milano, Italy.

Macromolecule Content 

  • Total Structure Weight: 48.59 kDa 
  • Atom Count: 3,428 
  • Modeled Residue Count: 439 
  • Deposited Residue Count: 440 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BCR P10015 heavy chainA [auth H]225Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
BCR P10015 light chainB [auth L]215Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth A]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.235 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.952α = 90
b = 99.952β = 90
c = 123.048γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItalyIG25764
Italian Association for Cancer ResearchItalyIG17032
Worldwide Cancer ResearchUnited Kingdom19-0096
Italian Ministry of HealthItalyRF-2018-12368231

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Database references
  • Version 1.2: 2026-02-18
    Changes: Database references