2RE9

Crystal structure of TL1A at 2.1 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.bbrc.2007.09.097
  • Primary Citation of Related Structures:  

  • 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 similar ...

    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.


    Related Citations: 
    • Purification and crystallization of recombinant human TNF-like ligand TL1A
      Jin, T.C.,Guo, F.,Kim, S.,Howard, A.J.,Zhang, Y.Z.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TNF superfamily ligand TL1A
A, B, C
181Homo sapiensMutation(s): 0 
Gene Names: TNFSF15 (TL1, VEGI)
Find proteins for O95150 (Homo sapiens)
Go to Gene View: TNFSF15
Go to UniProtKB:  O95150
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.198 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 114.911α = 90.00
b = 114.911β = 90.00
c = 119.346γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MAR345data collection
CNSrefinement
PDB_EXTRACTdata extraction
PHASERphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description