6FXN

Crystal structure of human BAFF in complex with Fab fragment of anti-BAFF antibody belimumab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A loop region of BAFF controls B cell survival and regulates recognition by different inhibitors.

Vigolo, M.Chambers, M.G.Willen, L.Chevalley, D.Maskos, K.Lammens, A.Tardivel, A.Das, D.Kowalczyk-Quintas, C.Schuepbach-Mallepell, S.Smulski, C.R.Eslami, M.Rolink, A.Hummler, E.Samy, E.Fomekong Nanfack, Y.Mackay, F.Liao, M.Hess, H.Jiang, X.Schneider, P.

(2018) Nat Commun 9: 1199-1199

  • DOI: https://doi.org/10.1038/s41467-018-03323-8
  • Primary Citation of Related Structures:  
    6FXN

  • PubMed Abstract: 

    The B cell survival factor (TNFSF13B/BAFF) is often elevated in autoimmune diseases and is targeted in the clinic for the treatment of systemic lupus erythematosus. BAFF contains a loop region designated the flap, which is dispensable for receptor binding. Here we show that the flap of BAFF has two functions. In addition to facilitating the formation of a highly active BAFF 60-mer as shown previously, it also converts binding of BAFF to TNFRSF13C (BAFFR) into a signaling event via oligomerization of individual BAFF-BAFFR complexes. Binding and activation of BAFFR can therefore be targeted independently to inhibit or activate the function of BAFF. Moreover, structural analyses suggest that the flap of BAFF 60-mer temporarily prevents binding of an anti-BAFF antibody (belimumab) but not of a decoy receptor (atacicept). The observed differences in profiles of BAFF inhibition may confer distinct biological and clinical efficacies to these therapeutically relevant inhibitors.


  • Organizational Affiliation

    Department of Biochemistry, University of Lausanne, 1066, Epalinges, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor ligand superfamily member 13B
A, B, C, J, K
A, B, C, J, K, L
164Homo sapiensMutation(s): 1 
Gene Names: TNFSF13BBAFFBLYSTALL1TNFSF20ZTNF4UNQ401/PRO738
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y275 (Homo sapiens)
Explore Q9Y275 
Go to UniProtKB:  Q9Y275
PHAROS:  Q9Y275
GTEx:  ENSG00000102524 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y275
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
belimumab heavy chain
D, F, H, M, O
D, F, H, M, O, Q
225Homo sapiensMutation(s): 0 
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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
belimumab light chain
E, G, I, N, P
E, G, I, N, P, R
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.687α = 90
b = 135.499β = 91.88
c = 138.18γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary