4EN0

Crystal structure of light


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanistic basis for functional promiscuity in the TNF and TNF receptor superfamilies: structure of the LIGHT:DcR3 assembly.

Liu, W.Zhan, C.Cheng, H.Kumar, P.R.Bonanno, J.B.Nathenson, S.G.Almo, S.C.

(2014) Structure 22: 1252-1262

  • DOI: 10.1016/j.str.2014.06.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • LIGHT initiates intracellular signaling via engagement of the two TNF receptors, HVEM and LTβR. In humans, LIGHT is neutralized by DcR3, a unique soluble member of the TNFR superfamily, which tightly binds LIGHT and inhibits its interactions with HVE ...

    LIGHT initiates intracellular signaling via engagement of the two TNF receptors, HVEM and LTβR. In humans, LIGHT is neutralized by DcR3, a unique soluble member of the TNFR superfamily, which tightly binds LIGHT and inhibits its interactions with HVEM and LTβR. DcR3 also neutralizes two other TNF ligands, FasL and TL1A. Due to its ability to neutralize three distinct different ligands, DcR3 contributes to a wide range of biological and pathological processes, including cancer and autoimmune diseases. However, the mechanisms that support the broad specificity of DcR3 remain to be fully defined. We report the structures of LIGHT and the LIGHT:DcR3 complex, which reveal the structural basis for the DcR3-mediated neutralization of LIGHT and afford insights into DcR3 function and binding promiscuity. Based on these structures, we designed LIGHT mutants with altered affinities for DcR3 and HVEM, which may represent mechanistically informative probe reagents.


    Organizational Affiliation

    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor ligand superfamily member 14
A, B, C
167Homo sapiensMutation(s): 0 
Gene Names: TNFSF14 (HVEML, LIGHT)
Find proteins for O43557 (Homo sapiens)
Go to Gene View: TNFSF14
Go to UniProtKB:  O43557
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.234 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 94.699α = 90.00
b = 99.981β = 90.00
c = 124.382γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2014-12-31
    Type: Database references