6O3C | pdb_00006o3c

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

• PDB DOI: https://doi.org/10.2210/pdb6O3C/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus, Lama glama
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2019-02-26 Released: 2019-07-03 
• Deposition Author(s): Deshpande, I.S., 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.
• Funding Organization(s): National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.294 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Models: experimental

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

• PubMed: 31263273 
• DOI: https://doi.org/10.1038/s41586-019-1355-4
• Primary Citation Related Structures: 
  6O3C


• PubMed Abstract: 
  

  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.

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Organizational Affiliation: 
• Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.
Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, USA.
Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA.
Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
Department of Computer Science, Stanford University, Stanford, CA, USA.
Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
Biophysics Program, Stanford University, Stanford, CA, USA.
Department of Urology, Stanford University School of Medicine, Stanford, CA, USA.
Chemical and Systems 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. [e-mail].
Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, USA. [e-mail].
Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA. [e-mail].
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA. [e-mail].
Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.05 kDa 
• Atom Count: 4,902 
• Modeled Residue Count: 606 
• Deposited Residue Count: 653 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Smoothened homolog	A	525	Mus musculus	Mutation(s): 0  Gene Names: Smo, Smoh Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P56726 (Mus musculus) Explore P56726  Go to UniProtKB:  P56726
IMPC:  MGI:108075
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P56726-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NbSmo8	B	128	Lama glama	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LKD	M [auth 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
CLR	N [auth A], O [auth A]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
OLB	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-QJRAZLAKSA-N
NAG	K [auth A], L [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.294 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.01	α = 90
b = 121.09	β = 90
c = 157.01	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Deshpande, I.S., 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.

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Funding Organization	Location	Grant Number
National Institutes of Health/Office of the Director	United States	DP5-OD023048-01

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Database references
• Version 1.2: 2019-07-24
  Changes: Data collection, Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-10-23
  Changes: Structure summary