2RE9 | pdb_00002re9

Crystal structure of TL1A at 2.1 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.253 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.199 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2RE9

This is version 1.4 of the entry. See complete history

Literature

X-ray crystal structure of TNF ligand family member TL1A at 2.1 A.

Jin, T.Guo, F.Kim, S.Howard, A.Zhang, Y.Z.

(2007) Biochem Biophys Res Commun 364: 1-6

  • DOI: https://doi.org/10.1016/j.bbrc.2007.09.097
  • Primary Citation Related Structures: 
    2O0O, 2RE9

  • PubMed Abstract: 

    The TNF family has been one of the most intensively studied protein families in the past two decades and it has rapidly expanded through the era of genomics and bioinformatics. However, the structural basis of the functional and interactional similarities and differences of this family is poorly understood. TL1A is a recently identified TNF family member that has received increasing attention. Here, the crystal structure of human TL1A is reported. TL1A forms a homotrimer with each monomer assuming a jellyroll beta-sandwich fold. The CD loop in TL1A is the longest among the TNF ligand members with known structure and the AA' loop in TL1A is the second longest after that in TRAIL, where part of it is disordered. Both these loops are known to participate in receptor binding in TNFbeta/LTalpha. The AA' loop may be very different in other TL1A variants if the overall fold is to be preserved.


  • Organizational Affiliation
    • Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA.

Macromolecule Content 

  • Total Structure Weight: 61.87 kDa 
  • Atom Count: 4,458 
  • Modeled Residue Count: 492 
  • Deposited Residue Count: 543 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TNF superfamily ligand TL1A
A, B, C
181Homo sapiensMutation(s): 0 
Gene Names: TNFSF15
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
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.253 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.199 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.911α = 90
b = 114.911β = 90
c = 119.346γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MAR345data collection
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary