4MXW

Structure of heterotrimeric lymphotoxin LTa1b2 bound to lymphotoxin beta receptor LTbR and anti-LTa Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dimerization of LT beta R by LT alpha 1 beta 2 is necessary and sufficient for signal transduction.

Sudhamsu, J.Yin, J.Chiang, E.Y.Starovasnik, M.A.Grogan, J.L.Hymowitz, S.G.

(2013) Proc.Natl.Acad.Sci.USA 110: 19896-19901

  • DOI: 10.1073/pnas.1310838110
  • Primary Citation of Related Structures:  4MXV

  • PubMed Abstract: 
  • Homotrimeric TNF superfamily ligands signal by inducing trimers of their cognate receptors. As a biologically active heterotrimer, Lymphotoxin(LT)α1β2 is unique in the TNF superfamily. How the three unique potential receptor-binding interfaces in LTα ...

    Homotrimeric TNF superfamily ligands signal by inducing trimers of their cognate receptors. As a biologically active heterotrimer, Lymphotoxin(LT)α1β2 is unique in the TNF superfamily. How the three unique potential receptor-binding interfaces in LTα1β2 trigger signaling via LTβ Receptor (LTβR) resulting in lymphoid organogenesis and propagation of inflammatory signals is poorly understood. Here we show that LTα1β2 possesses two binding sites for LTβR with distinct affinities and that dimerization of LTβR by LTα1β2 is necessary and sufficient for signal transduction. The crystal structure of a complex formed by LTα1β2, LTβR, and the fab fragment of an antibody that blocks LTβR activation reveals the lower affinity receptor-binding site. Mutations targeting each potential receptor-binding site in an engineered single-chain variant of LTα1β2 reveal the high-affinity site. NF-κB reporter assays further validate that disruption of receptor interactions at either site is sufficient to prevent signaling via LTβR.


    Organizational Affiliation

    Departments of Structural Biology and Immunology, Genentech, Inc., South San Francisco, CA 94080.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor receptor superfamily member 3
S, R
193Homo sapiensGene Names: LTBR (D12S370, TNFCR, TNFR3, TNFRSF3)
Find proteins for P36941 (Homo sapiens)
Go to Gene View: LTBR
Go to UniProtKB:  P36941
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lymphotoxin-alpha
X, A
157Homo sapiensGene Names: LTA (TNFB, TNFSF1)
Find proteins for P01374 (Homo sapiens)
Go to Gene View: LTA
Go to UniProtKB:  P01374
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Lymphotoxin-beta
Y, Z, B, D
210Homo sapiensGene Names: LTB (TNFC, TNFSF3)
Find proteins for Q06643 (Homo sapiens)
Go to Gene View: LTB
Go to UniProtKB:  Q06643
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
anti-Lymphotoxin alpha antibody heavy chain
W, H
213N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
anti-Lymphotoxin alpha antibody light chain
V, L
211N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.231 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 211.201α = 90.00
b = 52.428β = 101.10
c = 253.241γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
ADSCdata collection
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2013-12-11
    Type: Database references
  • Version 1.2: 2013-12-18
    Type: Database references