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 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 2.0 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 U S A 110: 20461

  • DOI: 10.1073/pnas.1317002110
  • Primary Citation of Related Structures:  
    4BV4

  • 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 molecules such as bacterial endotoxin ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN SPAETZLE C-106A [auth L], B [auth M]107Drosophila melanogasterMutation(s): 0 
Gene Names: spzCG6134
UniProt
Find proteins for P48607 (Drosophila melanogaster)
Explore P48607 
Go to UniProtKB:  P48607
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN TOLL, VARIABLE LYMPHOCYTE RECEPTOR B CHIMERAC [auth R]446Drosophila melanogasterEptatretus burgeri
This entity is chimeric
Mutation(s): 0 
Gene Names: TlVLRB
EC: 3.2.2.6
UniProt
Find proteins for Q4G1L2 (Eptatretus burgeri)
Explore Q4G1L2 
Go to UniProtKB:  Q4G1L2
Find proteins for P08953 (Drosophila melanogaster)
Explore P08953 
Go to UniProtKB:  P08953
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth A]8N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G50714RV
GlyCosmos:  G50714RV
GlyGen:  G50714RV
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth R], F [auth R], G [auth R], H [auth R]2-acetamido-2-deoxy-beta-D-glucopyranose
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 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 198.31α = 90
b = 57.11β = 97.76
c = 70.5γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
ANISOSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2013-12-11
    Changes: Database references
  • Version 1.2: 2014-01-08
    Changes: Database references
  • Version 1.3: 2017-03-15
    Changes: Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary