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 
  • R-Value Observed: 0.201 

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:  
    2HFG, 2HFF

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CB3s Fab light chain (kappa)L214Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CB3s Fab heavy chainH232Homo sapiensMutation(s): 0 
Gene Names: DKFZp686I04196
Find proteins for Q6N093 (Homo sapiens)
Explore Q6N093 
Go to UniProtKB:  Q6N093
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 13CR51Homo sapiensMutation(s): 2 
Gene Names: TNFRSF13CBAFFRBR3
Find proteins for Q96RJ3 (Homo sapiens)
Explore Q96RJ3 
Go to UniProtKB:  Q96RJ3
NIH Common Fund Data Resources
PHAROS  Q96RJ3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.201 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.408α = 90
b = 146.408β = 90
c = 146.408γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance