2HFG

Crystal structure of hBR3 bound to CB3s-Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthetic anti-BR3 antibodies that mimic BAFF binding and target both human and murine B cells.

Lee, C.V.Hymowitz, S.G.Wallweber, H.J.Gordon, N.C.Billeci, K.L.Tsai, S.P.Compaan, D.M.Yin, J.Gong, Q.Kelley, R.F.Deforge, L.E.Martin, F.Starovasnik, M.A.Fuh, G.

(2006) Blood 108: 3103-3111

  • DOI: 10.1182/blood-2006-03-011031
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • BR3, which is expressed on all mature B cells, is a specific receptor for the B-cell survival and maturation factor BAFF (B-cell-activating factor belonging to the tumor necrosis factor [TNF] family). In order to investigate the consequences of targe ...

    BR3, which is expressed on all mature B cells, is a specific receptor for the B-cell survival and maturation factor BAFF (B-cell-activating factor belonging to the tumor necrosis factor [TNF] family). In order to investigate the consequences of targeting BR3 in murine models and to assess the potential of BR3 antibodies as human therapeutics, synthetic antibody phage libraries were employed to identify BAFF-blocking antibodies cross-reactive to murine and human BR3, which share 52% identity in their extracellular domains. We found an antibody, CB1, which exhibits muM affinity for murine BR3 and very weak affinity for the human receptor. CB3s, an affinity-matured variant of CB1, has sub-nM affinity for BR3 from both species. Alanine scanning and crystallographic structural analysis of the CB3s/BR3 complex reveal that CB3s mimics BAFF by interacting with a similar region of the BR3 surface. Despite this similarity in binding epitopes, CB1 variants antagonize BAFF-dependent human B-cell proliferation in vitro and are effective at reducing murine B-cell populations in vivo, showing significant promise as therapeutics for human B-cell-mediated diseases.


    Organizational Affiliation

    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CB3s Fab light chain (kappa)
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CB3s Fab heavy chain
H
232N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor receptor superfamily member 13C
R
51Homo sapiensMutation(s): 2 
Gene Names: TNFRSF13C (BAFFR, BR3)
Find proteins for Q96RJ3 (Homo sapiens)
Go to Gene View: TNFRSF13C
Go to UniProtKB:  Q96RJ3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 146.408α = 90.00
b = 146.408β = 90.00
c = 146.408γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-06-23 
  • Released Date: 2006-11-07 
  • Deposition Author(s): Hymowitz, S.G.

Revision History 

  • Version 1.0: 2006-11-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance