4LXS

Structure of the Toll - Spatzle complex, a molecular hub in Drosophila development and innate immunity (glycosylated form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structure of the Toll-Spatzle complex, a molecular hub in Drosophila development and innate immunity.

Parthier, C.Stelter, M.Ursel, C.Fandrich, U.Lilie, H.Breithaupt, C.Stubbs, M.T.

(2014) Proc Natl Acad Sci U S A 111: 6281-6286

  • DOI: https://doi.org/10.1073/pnas.1320678111
  • Primary Citation of Related Structures:  
    4LXR, 4LXS

  • PubMed Abstract: 

    Drosophila Toll receptors are involved in embryonic development and the immune response of adult flies. In both processes, the only known Toll receptor ligand is the human nerve growth factor-like cystine knot protein Spätzle. Here we present the crystal structure of a 1:1 (nonsignaling) complex of the full-length Toll receptor ectodomain (ECD) with the Spätzle cystine knot domain dimer. The ECD is divided into two leucine-rich repeat (LRR) domains, each of which is capped by cysteine-rich domains. Spätzle binds to the concave surface of the membrane-distal LRR domain, in contrast to the flanking ligand interactions observed for mammalian Toll-like receptors, with asymmetric contributions from each Spätzle protomer. The structure allows rationalization of existing genetic and biochemical data and provides a framework for targeting the immune systems of insects of economic importance, as well as a variety of invertebrate disease vectors.


  • Organizational Affiliation

    Institut für Biochemie und Biotechnologie and Mitteldeutsches Zentrum für Struktur und Dynamik von Proteinen, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein toll783Drosophila melanogasterMutation(s): 0 
Gene Names: TlCG5490
UniProt
Find proteins for P08953 (Drosophila melanogaster)
Explore P08953 
Go to UniProtKB:  P08953
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08953
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein spaetzle C-106B [auth J],
C [auth K]
114Drosophila melanogasterMutation(s): 0 
Gene Names: spzCG6134
UniProt
Find proteins for P48607 (Drosophila melanogaster)
Explore P48607 
Go to UniProtKB:  P48607
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48607
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth B]5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G52322TF
GlyCosmos:  G52322TF
GlyGen:  G52322TF
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C],
G [auth E],
H [auth F],
I [auth G],
J [auth H]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth D]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.278α = 90
b = 76.824β = 126.29
c = 123.822γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
SHARPphasing
SOLOMONphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-05-21
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary