1DU3

Crystal structure of TRAIL-SDR5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of TRAIL-DR5 complex identifies a critical role of the unique frame insertion in conferring recognition specificity

Cha, S.-S.Sung, B.-J.Kim, Y.A.Song, Y.L.Kim, H.J.Kim, S.Lee, M.S.Oh, B.-H.

(2000) J Biol Chem 275: 31171-31177

  • DOI: 10.1074/jbc.M004414200
  • Primary Citation of Related Structures:  
    1DU3

  • PubMed Abstract: 
  • TRAIL is a cytokine that induces apoptosis in a wide variety of tumor cells but rarely in normal cells. It contains an extraordinarily elongated loop because of an unique insertion of 12-16 amino acids compared with the other members of tumor necrosis factor family ...

    TRAIL is a cytokine that induces apoptosis in a wide variety of tumor cells but rarely in normal cells. It contains an extraordinarily elongated loop because of an unique insertion of 12-16 amino acids compared with the other members of tumor necrosis factor family. Biological implication of the frame insertion has not been clarified. We have determined the crystal structure of TRAIL in a complex with the extracellular domain of death receptor DR5 at 2.2 A resolution. The structure reveals extensive contacts between the elongated loop and DR5 in an interaction mode that would not be allowed without the frame insertion. These interactions are missing in the structures of the complex determined by others recently. This observation, along with structure-inspired deletion analysis, identifies the critical role of the frame insertion as a molecular strategy conferring specificity upon the recognition of cognate receptors. The structure also suggests that a built-in flexibility of the tumor necrosis factor receptor family members is likely to play a general and important role in the binding and recognition of tumor necrosis factor family members.


    Organizational Affiliation

    Department of Life Science, and Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang, Kyungbuk, 790-784, Korea.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DEATH RECEPTOR 5A, B, C, G, H, I130Homo sapiensMutation(s): 0 
Gene Names: TNFRSF10BDR5KILLERTRAILR2TRICK2ZTNFR9UNQ160/PRO186
Find proteins for O14763 (Homo sapiens)
Explore O14763 
Go to UniProtKB:  O14763
NIH Common Fund Data Resources
PHAROS:  O14763
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TNF-RELATED APOPTOSIS INDUCING LIGANDD, E, F, J, K, L168Homo sapiensMutation(s): 0 
Gene Names: TNFSF10APO2LTRAIL
Find proteins for P50591 (Homo sapiens)
Explore P50591 
Go to UniProtKB:  P50591
NIH Common Fund Data Resources
PHAROS:  P50591
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
M [auth E], N [auth K]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.63α = 90
b = 124.81β = 104.489
c = 128.37γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-09-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation