3K48

Crystal structure of APRIL bound to a peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Multiple novel classes of APRIL-specific receptor-blocking peptides isolated by phage display.

Gordon, N.C.Lien, S.Johnson, J.Wallweber, H.J.Tran, T.Currell, B.Mathieu, M.Quan, C.Starovasnik, M.A.Hymowitz, S.G.Kelley, R.F.

(2010) J.Mol.Biol. 396: 166-177

  • DOI: 10.1016/j.jmb.2009.11.041

  • PubMed Abstract: 
  • A proliferation-inducing ligand (APRIL) is a member of the tumor necrosis factor (TNF) ligand superfamily and has a proliferative effect on both normal and tumor cells. The TNF family receptors (B-cell maturation antigen (BCMA), transmembrane activat ...

    A proliferation-inducing ligand (APRIL) is a member of the tumor necrosis factor (TNF) ligand superfamily and has a proliferative effect on both normal and tumor cells. The TNF family receptors (B-cell maturation antigen (BCMA), transmembrane activator and CAML-interactor (TACI), and BAFF receptor-3 (BR3)) for APRIL and the closely related ligand, B-cell activating factor of the TNF family (BAFF), bind these ligands through a highly conserved six residue DXL motif ((F/Y/W)-D-X-L-(V/T)-(R/G)). Panning peptide phage display libraries led to the identification of several novel classes of APRIL-binding peptides, which could be grouped by their common sequence motifs. Interestingly, only one of these ten classes consisted of peptides containing the DXL motif. Nevertheless, all classes of peptides prevented APRIL, but not BAFF, from binding BCMA, their shared receptor. Synthetic peptides based on selected sequences inhibited APRIL binding to BCMA with IC(50) values of 0.49-27 microM. An X-ray crystallographic structure of APRIL bound to one of the phage-derived peptides showed that the peptide, lacking the DXL motif, was nevertheless bound in the DXL pocket on APRIL. Our results demonstrate that even though a focused, highly conserved motif is required for APRIL-receptor interaction, remarkably, many novel and distinct classes of peptides are also capable of binding APRIL at the ligand receptor interface.


    Organizational Affiliation

    Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor ligand superfamily member 13
A, B, D
140Mus musculusMutation(s): 0 
Gene Names: Tnfsf13 (April)
Find proteins for Q9D777 (Mus musculus)
Go to UniProtKB:  Q9D777
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide
R, S, T
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.811α = 90.00
b = 84.771β = 99.45
c = 55.562γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-10-05 
  • Released Date: 2009-11-24 
  • Deposition Author(s): Hymowitz, S.G.

Revision History 

  • Version 1.0: 2009-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2011-08-10
    Type: Database references