5KZZ

Crystal structure of the xenopus Smoothened cysteine-rich domain (CRD) in its apo-form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Cellular Cholesterol Directly Activates Smoothened in Hedgehog Signaling.

Huang, P.Nedelcu, D.Watanabe, M.Jao, C.Kim, Y.Liu, J.Salic, A.

(2016) Cell 166: 1176-1187.e14

  • DOI: https://doi.org/10.1016/j.cell.2016.08.003
  • Primary Citation of Related Structures:  
    5KZV, 5KZY, 5KZZ

  • PubMed Abstract: 

    In vertebrates, sterols are necessary for Hedgehog signaling, a pathway critical in embryogenesis and cancer. Sterols activate the membrane protein Smoothened by binding its extracellular, cysteine-rich domain (CRD). Major unanswered questions concern the nature of the endogenous, activating sterol and the mechanism by which it regulates Smoothened. We report crystal structures of CRD complexed with sterols and alone, revealing that sterols induce a dramatic conformational change of the binding site, which is sufficient for Smoothened activation and is unique among CRD-containing receptors. We demonstrate that Hedgehog signaling requires sterol binding to Smoothened and define key residues for sterol recognition and activity. We also show that cholesterol itself binds and activates Smoothened. Furthermore, the effect of oxysterols is abolished in Smoothened mutants that retain activation by cholesterol and Hedgehog. We propose that the endogenous Smoothened activator is cholesterol, not oxysterols, and that vertebrate Hedgehog signaling controls Smoothened by regulating its access to cholesterol.


  • Organizational Affiliation

    Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Smoothened127Xenopus laevisMutation(s): 0 
Gene Names: Smo
UniProt
Find proteins for Q98SW5 (Xenopus laevis)
Explore Q98SW5 
Go to UniProtKB:  Q98SW5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ98SW5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A],
I [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.656α = 90
b = 37.352β = 97.46
c = 43.151γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRO1GM092924
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRO1GM110041

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-06
    Changes: Structure summary