3K51

Crystal Structure of DcR3-TL1A complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Decoy Strategies: The Structure of TL1A:DcR3 Complex.

Zhan, C.Patskovsky, Y.Yan, Q.Li, Z.Ramagopal, U.Cheng, H.Brenowitz, M.Hui, X.Nathenson, S.G.Almo, S.C.

(2011) Structure 19: 162-171

  • DOI: 10.1016/j.str.2010.12.004
  • Primary Citation of Related Structures:  
    3K51, 3MHD, 3MI8

  • PubMed Abstract: 
  • Decoy Receptor 3 (DcR3), a secreted member of the Tumor Necrosis Factor (TNF) receptor superfamily, neutralizes three different TNF ligands: FasL, LIGHT, and TL1A. Each of these ligands engages unique signaling receptors which direct distinct and critical immune responses ...

    Decoy Receptor 3 (DcR3), a secreted member of the Tumor Necrosis Factor (TNF) receptor superfamily, neutralizes three different TNF ligands: FasL, LIGHT, and TL1A. Each of these ligands engages unique signaling receptors which direct distinct and critical immune responses. We report the crystal structures of the unliganded DcR3 ectodomain and its complex with TL1A, as well as complementary mutagenesis and biochemical studies. These analyses demonstrate that DcR3 interacts with invariant backbone and side-chain atoms in the membrane-proximal half of TL1A which supports recognition of its three distinct TNF ligands. Additional features serve as antideterminants that preclude interaction with other members of the TNF superfamily. This mode of interaction is unique among characterized TNF:TNFR family members and provides a mechanistic basis for the broadened specificity required to support the decoy function of DcR3, as well as for the rational manipulation of specificity and affinity of DcR3 and its ligands.


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tumor necrosis factor ligand superfamily member 15, secreted formA184Homo sapiensMutation(s): 2 
Gene Names: TL1TNFSF15VEGI
UniProt & NIH Common Fund Data Resources
Find proteins for O95150 (Homo sapiens)
Explore O95150 
Go to UniProtKB:  O95150
PHAROS:  O95150
GTEx:  ENSG00000181634 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95150
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Decoy receptor 3B176Homo sapiensMutation(s): 0 
Gene Names: DCR3TNFRSF6BTR6UNQ186/PRO212
UniProt & NIH Common Fund Data Resources
Find proteins for O95407 (Homo sapiens)
Explore O95407 
Go to UniProtKB:  O95407
PHAROS:  O95407
GTEx:  ENSG00000243509 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95407
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.89α = 90
b = 74.89β = 90
c = 143.125γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2021-10-13
    Changes: Database references