6O3C

Crystal structure of active Smoothened bound to SAG21k, cholesterol, and NbSmo8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Smoothened stimulation by membrane sterols drives Hedgehog pathway activity.

Deshpande, I.Liang, J.Hedeen, D.Roberts, K.J.Zhang, Y.Ha, B.Latorraca, N.R.Faust, B.Dror, R.O.Beachy, P.A.Myers, B.R.Manglik, A.

(2019) Nature 571: 284-288

  • DOI: 10.1038/s41586-019-1355-4

  • PubMed Abstract: 
  • Hedgehog signalling is fundamental to embryonic development and postnatal tissue regeneration <sup>1 </sup>. Aberrant postnatal Hedgehog signalling leads to several malignancies, including basal cell carcinoma and paediatric medulloblastoma <sup>2 </ ...

    Hedgehog signalling is fundamental to embryonic development and postnatal tissue regeneration 1 . Aberrant postnatal Hedgehog signalling leads to several malignancies, including basal cell carcinoma and paediatric medulloblastoma 2 . Hedgehog proteins bind to and inhibit the transmembrane cholesterol transporter Patched-1 (PTCH1), which permits activation of the seven-transmembrane transducer Smoothened (SMO) via a mechanism that is poorly understood. Here we report the crystal structure of active mouse SMO bound to both the agonist SAG21k and to an intracellular binding nanobody that stabilizes a physiologically relevant active state. Analogous to other G protein-coupled receptors, the activation of SMO is associated with subtle motions in the extracellular domain, and larger intracellular changes. In contrast to recent models 3-5 , a cholesterol molecule that is critical for SMO activation is bound deep within the seven-transmembrane pocket. We propose that the inactivation of PTCH1 by Hedgehog allows a transmembrane sterol to access this seven-transmembrane site (potentially through a hydrophobic tunnel), which drives the activation of SMO. These results-combined with signalling studies and molecular dynamics simulations-delineate the structural basis for PTCH1-SMO regulation, and suggest a strategy for overcoming clinical resistance to SMO inhibitors.


    Organizational Affiliation

    Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA. Benjamin.Myers@hci.utah.edu.,Department of Urology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Computer Science, Stanford University, Stanford, CA, USA.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, USA. Benjamin.Myers@hci.utah.edu.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, USA. Aashish.Manglik@ucsf.edu.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA. Aashish.Manglik@ucsf.edu.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA.,Biophysics Program, Stanford University, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA. Benjamin.Myers@hci.utah.edu.,Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Smoothened homolog
A
525Mus musculusMutation(s): 0 
Gene Names: Smo (Smoh)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Smoothened (SMO) receptor bound to SAG21k, cholesterol, and NbSmo8
Find proteins for P56726 (Mus musculus)
Go to UniProtKB:  P56726
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NbSmo8
B
128N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLB
Query on OLB

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Download CCD File 
A
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
LKD
Query on LKD

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Download CCD File 
A
3-chloro-4,7-difluoro-N-{[2-methoxy-5-(pyridin-4-yl)phenyl]methyl}-N-[trans-4-(methylamino)cyclohexyl]-1-benzothiophene-2-carboxamide
C29 H28 Cl F2 N3 O2 S
YVIFQUJDZSAFKG-MEMLXQNLSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CLR
Query on CLR

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Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.245 
  • Space Group: P 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 39.010α = 90.00
b = 121.090β = 90.00
c = 157.010γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesDP5-OD023048-01

Revision History 

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-07-17
    Type: Data collection, Database references
  • Version 1.2: 2019-07-24
    Type: Data collection, Database references