4BV4

Structure and allostery in Toll-Spatzle recognition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Cytokine Spatzle Binds to the Drosophila Immunoreceptor Toll with a Neurotrophin-Like Specificity and Couples Receptor Activation.

Lewis, M.Arnot, C.J.Beeston, H.Mccoy, A.Ashcroft, A.E.Gay, N.J.Gangloff, M.

(2013) Proc.Natl.Acad.Sci.USA 110: 20461

  • DOI: 10.1073/pnas.1317002110

  • PubMed Abstract: 
  • Drosophila Toll functions in embryonic development and innate immunity and is activated by an endogenous ligand, Spätzle (Spz). The related Toll-like receptors in vertebrates also function in immunity but are activated directly by pathogen-associated ...

    Drosophila Toll functions in embryonic development and innate immunity and is activated by an endogenous ligand, Spätzle (Spz). The related Toll-like receptors in vertebrates also function in immunity but are activated directly by pathogen-associated molecules such as bacterial endotoxin. Here, we present the crystal structure at 2.35-Å resolution of dimeric Spz bound to a Toll ectodomain encompassing the first 13 leucine-rich repeats. The cystine knot of Spz binds the concave face of the Toll leucine-rich repeat solenoid in an area delineated by N-linked glycans and induces a conformational change. Mutagenesis studies confirm that the interface observed in the crystal structure is relevant for signaling. The asymmetric binding mode of Spz to Toll is similar to that of nerve growth factor (NGF) in complex with the p75 neurotrophin receptor but is distinct from that of microbial ligands bound to the Toll-like receptors. Overall, this study indicates an allosteric signaling mechanism for Toll in which ligand binding to the N terminus induces a conformational change that couples to homodimerization of juxtamembrane structures in the Toll ectodomain C terminus.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN SPAETZLE C-106
L, M
107Drosophila melanogasterMutation(s): 0 
Gene Names: spz
Find proteins for P48607 (Drosophila melanogaster)
Go to UniProtKB:  P48607
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN TOLL, VARIABLE LYMPHOCYTE RECEPTOR B CHIMERA
R
446Drosophila melanogasterEptatretus burgeri
This entity is chimeric
Mutation(s): 0 
Gene Names: Tl, VLRB
Find proteins for P08953 (Drosophila melanogaster)
Go to UniProtKB:  P08953
Find proteins for Q4G1L2 (Eptatretus burgeri)
Go to UniProtKB:  Q4G1L2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
R
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
R
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 198.310α = 90.00
b = 57.110β = 97.76
c = 70.500γ = 90.00
Software Package:
Software NamePurpose
ANISOSCALEdata scaling
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2013-12-11
    Type: Database references
  • Version 1.2: 2014-01-08
    Type: Database references
  • Version 1.3: 2017-03-15
    Type: Source and taxonomy