3UP0

Nuclear receptor DAF-12 from hookworm Ancylostoma ceylanicum in complex with (25S)-delta7-dafachronic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Conservation of Ligand Binding Reveals a Bile Acid-like Signaling Pathway in Nematodes.

Zhi, X.Zhou, X.E.Melcher, K.Motola, D.L.Gelmedin, V.Hawdon, J.Kliewer, S.A.Mangelsdorf, D.J.Xu, H.E.

(2012) J Biol Chem 287: 4894-4903

  • DOI: 10.1074/jbc.M111.315242
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Bile acid-like molecules named dafachronic acids (DAs) control the dauer formation program in Caenorhabditis elegans through the nuclear receptor DAF-12. This mechanism is conserved in parasitic nematodes to regulate their dauer-like infective larval ...

    Bile acid-like molecules named dafachronic acids (DAs) control the dauer formation program in Caenorhabditis elegans through the nuclear receptor DAF-12. This mechanism is conserved in parasitic nematodes to regulate their dauer-like infective larval stage, and as such, the DAF-12 ligand binding domain has been identified as an important therapeutic target in human parasitic hookworm species that infect more than 600 million people worldwide. Here, we report two x-ray crystal structures of the hookworm Ancylostoma ceylanicum DAF-12 ligand binding domain in complex with DA and cholestenoic acid (a bile acid-like metabolite), respectively. Structure analysis and functional studies reveal key residues responsible for species-specific ligand responses of DAF-12. Furthermore, DA binds to DAF-12 mechanistically and is structurally similar to bile acids binding to the mammalian bile acid receptor farnesoid X receptor. Activation of DAF-12 by cholestenoic acid and the cholestenoic acid complex structure suggest that bile acid-like signaling pathways have been conserved in nematodes and mammals. Together, these results reveal the molecular mechanism for the interplay between parasite and host, provide a structural framework for DAF-12 as a promising target in treating nematode parasitism, and provide insight into the evolution of gut parasite hormone-signaling pathways.


    Organizational Affiliation

    Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
aceDAF-12A, B243Ancylostoma ceylanicumMutation(s): 0 
Gene Names: daf-12
Find proteins for H0USY8 (Ancylostoma ceylanicum)
Explore H0USY8 
Go to UniProtKB:  H0USY8
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 2P, Q14Homo sapiensMutation(s): 0 
Gene Names: NCOA2BHLHE75SRC2TIF2
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS  Q15596
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D7S
Query on D7S

Download CCD File 
A, B
(5beta,14beta,17alpha,25S)-3-oxocholest-7-en-26-oic acid
C27 H42 O3
SQTAVUCHOVVOFD-OBRBSRNPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.012α = 90
b = 85.163β = 107.1
c = 66.127γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
SCALEPACKdata scaling
PHASESphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2012-01-11
    Changes: Database references
  • Version 1.2: 2012-02-29
    Changes: Database references