1D2Q | pdb_00001d2q

CRYSTAL STRUCTURE OF HUMAN TRAIL

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.282 (Depositor) 
  • R-Value Work: 
    0.209 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history. 

Literature

2.8 A resolution crystal structure of human TRAIL, a cytokine with selective antitumor activity.

Cha, S.S., Kim, M.S., Choi, Y.H., Sung, B.J., Shin, N.K., Shin, H.C., Sung, Y.C., Oh, B.H.

(1999) Immunity 11: 253-261

  • DOI: https://doi.org/10.1016/s1074-7613(00)80100-4
  • Primary Citation Related Structures: 
    1D2Q

  • PubMed Abstract: 

    TRAIL is a newly identified cytokine belonging to the large tumor necrosis factor (TNF) family. TRAIL is a novel molecule inducing apoptosis in a wide variety of tumor cells but not in normal cells. To help in elucidating its biological roles and designing mutants with improved therapeutic potential, we have determined the crystal structure of human TRAIL. The structure reveals that a unique frame insertion of 12-16 amino acids adopts a salient loop structure penetrating into the receptor-binding site. The loop drastically alters the common receptor-binding surface of the TNF family most likely for the specific recognition of cognate partners. A structure-based mutagenesis study demonstrates a critical role of the insertion loop in the cytotoxic activity of TRAIL.

    • Organizational Affiliation: 
    • Department of Life Science and School of Environmental Engineering, Pohang University of Science and Technology, Kyungbuk, Korea.

Macromolecule Content 

  • Total Structure Weight: 39.04 kDa 
  • Atom Count: 2,166 
  • Modeled Residue Count: 268 
  • Deposited Residue Count: 336 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TNF-RELATED APOPTOSIS INDUCING LIGAND
A, B
168Homo sapiensMutation(s): 0 
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.282 (Depositor) 
  • R-Value Work:  0.209 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.61α = 90
b = 65.61β = 90
c = 131.7γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2000-02-11 
    • Deposition Author(s): Cha, S.-S.

Revision History  (Full details and data files)

  • Version 1.0: 2000-02-11
    Type: Initial release
  • Version 1.1: 2008-04-02
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Structure summary