5CIR

Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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This is version 1.1 of the entry. See complete history. 


Literature

The structure of the death receptor 4-TNF-related apoptosis-inducing ligand (DR4-TRAIL) complex.

Ramamurthy, V., Yamniuk, A.P., Lawrence, E.J., Yong, W., Schneeweis, L.A., Cheng, L., Murdock, M., Corbett, M.J., Doyle, M.L., Sheriff, S.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1273-1281

  • DOI: https://doi.org/10.1107/S2053230X15016416
  • Primary Citation of Related Structures:  
    5CIR

  • PubMed Abstract: 

    The structure of death receptor 4 (DR4) in complex with TNF-related apoptosis-inducing ligand (TRAIL) has been determined at 3 Å resolution and compared with those of previously determined DR5-TRAIL complexes. Consistent with the high sequence similarity between DR4 and DR5, the overall arrangement of the DR4-TRAIL complex does not differ substantially from that of the DR5-TRAIL complex. However, subtle differences are apparent. In addition, solution interaction studies were carried out that show differences in the thermodynamics of binding DR4 or DR5 with TRAIL.

    • Organizational Affiliation: 

    Molecular Structure and Design, Bristol-Myers Squibb R&D, PO Box 4000, Princeton, NJ 08543-4000, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor ligand superfamily member 10A,
B,
C [auth D]		169Homo sapiensMutation(s): 0 
Gene Names: TNFSF10, APO2L, TRAIL
UniProt & NIH Common Fund Data Resources
Find proteins for P50591 (Homo sapiens)
Explore P50591 
Go to UniProtKB:  P50591
PHAROS:  P50591
GTEx:  ENSG00000121858 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50591
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 10AD [auth E],
E [auth F],
F [auth G]		108Homo sapiensMutation(s): 2 
Gene Names: TNFRSF10A, APO2, DR4, TRAILR1
UniProt & NIH Common Fund Data Resources
Find proteins for O00220 (Homo sapiens)
Explore O00220 
Go to UniProtKB:  O00220
PHAROS:  O00220
GTEx:  ENSG00000104689 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00220
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.6α = 90
b = 87.6β = 90
c = 107.7γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2017-01-18 
    • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description