5L7I

Structure of human Smoothened in complex with Vismodegib

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Structural basis of Smoothened regulation by its extracellular domains.

Byrne, E.F., Sircar, R., Miller, P.S., Hedger, G., Luchetti, G., Nachtergaele, S., Tully, M.D., Mydock-McGrane, L., Covey, D.F., Rambo, R.P., Sansom, M.S., Newstead, S., Rohatgi, R., Siebold, C.

(2016) Nature 535: 517-522

  • DOI: 10.1038/nature18934
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Developmental signals of the Hedgehog (Hh) and Wnt families are transduced across the membrane by Frizzledclass G-protein-coupled receptors (GPCRs) composed of both a heptahelical transmembrane domain (TMD) and an extracellular cysteine-rich domain ( ...

    Developmental signals of the Hedgehog (Hh) and Wnt families are transduced across the membrane by Frizzledclass G-protein-coupled receptors (GPCRs) composed of both a heptahelical transmembrane domain (TMD) and an extracellular cysteine-rich domain (CRD). How the large extracellular domains of GPCRs regulate signalling by the TMD is unknown. We present crystal structures of the Hh signal transducer and oncoprotein Smoothened, a GPCR that contains two distinct ligand-binding sites: one in its TMD and one in the CRD. The CRD is stacked a top the TMD, separated by an intervening wedge-like linker domain. Structure-guided mutations show that the interface between the CRD, linker domain and TMD stabilizes the inactive state of Smoothened. Unexpectedly, we find a cholesterol molecule bound to Smoothened in the CRD binding site. Mutations predicted to prevent cholesterol binding impair the ability of Smoothened to transmit native Hh signals. Binding of a clinically used antagonist, vismodegib, to the TMD induces a conformational change that is propagated to the CRD, resulting in loss of cholesterol from the CRD-linker domain-TMD interface. Our results clarify the structural mechanism by which the activity of a GPCR is controlled by ligand-regulated interactions between its extracellular and transmembrane domains.

    Organizational Affiliation: 

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Smoothened homolog,Soluble cytochrome b562,Smoothened homolog
A, B
638Homo sapiens, Escherichia coli
This entity is chimeric		Mutation(s): 0 
Gene Names: SMO (SMOH), cybC
Membrane protein
mpstruct		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
G Protein-Coupled Receptors (GPCRs)		Protein: 
Smoothened (SMO) receptor with bound antagonist, LY2940680
Find proteins for Q99835 (Homo sapiens)
Go to Gene View: SMO
Go to UniProtKB:  Q99835
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MPG
Query on MPG
Download SDF File 
Download CCD File 
B
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
 Ligand Interaction
VIS
Query on VIS
Download SDF File 
Download CCD File 
A, B
2-chloranyl-~{N}-(4-chloranyl-3-pyridin-2-yl-phenyl)-4-methylsulfonyl-benzamide
C19 H14 Cl2 N2 O3 S
BPQMGSKTAYIVFO-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VISIC50: 1.5 - 39 nM (94) BINDINGDB
VISKi: 16.2 nM (94) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.245 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 52.820α = 91.53
b = 71.290β = 98.20
c = 107.020γ = 105.92
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-07-27
    Type: Structure summary
  • Version 1.2: 2016-08-03
    Type: Database references
  • Version 1.3: 2016-08-10
    Type: Database references