Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 143.37 kDa 
• Atom Count: 9107 
• Modelled Residue Count: 1136 
• Deposited Residue Count: 1276 
• Unique protein chains: 1

5L7I

Structure of human Smoothened in complex with Vismodegib

• PDB DOI: 10.2210/pdb5L7I/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Escherichia coli
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2016-06-03 Released: 2016-07-20 
• Deposition Author(s): Byrne, E.X.B., Sircar, R., Miller, P.S., Hedger, G., Luchetti, G., Nachtergaele, S., Tully, M.D., Mydock-McGrane, L., Covey, D.F., Rambo, R.F., Sansom, M.S.P., Newstead, S., Rohatgi, R., Siebold, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.257 
• R-Value Work: 0.245 
• R-Value Observed: 0.245 

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

• PubMed: 27437577 
• DOI: 10.1038/nature18934
• Primary Citation of Related Structures:  
  5L7D, 5L7I


• 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 (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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Smoothened homolog,Soluble cytochrome b562,Smoothened homolog	A, B	638	Homo sapiens, Escherichia coli	Mutation(s): 0  Gene Names: SMO, SMOH, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for Q99835 (Homo sapiens) Explore Q99835  Go to UniProtKB:  Q99835
PHAROS:  Q99835 GTEx:  ENSG00000128602
UniProt Groups	P0ABE7Q99835

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VIS	D [auth A], F [auth B]	2-chloranyl-~{N}-(4-chloranyl-3-pyridin-2-yl-phenyl)-4-methylsulfonyl-benzamide C19 H14 Cl2 N2 O3 S BPQMGSKTAYIVFO-UHFFFAOYSA-N
MPG	G [auth B], H [auth B]	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate C21 H40 O4 JPJYKWFFJCWMPK-GDCKJWNLSA-N
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VIS	BindingDB:  5L7I	Ki: 16.2 (nM) from 1 assay(s)
		Kd: 9.8 (nM) from 1 assay(s)
		IC50: min: 0.4, max: 74 (nM) from 13 assay(s)
		EC50: min: 0.1, max: 4.7 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.257 
• R-Value Work: 0.245 
• R-Value Observed: 0.245 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.82	α = 91.53
b = 71.29	β = 98.2
c = 107.02	γ = 105.92

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-06-03 
• Released Date: 2016-07-20 
Deposition Author(s): Byrne, E.X.B., Sircar, R., Miller, P.S., Hedger, G., Luchetti, G., Nachtergaele, S., Tully, M.D., Mydock-McGrane, L., Covey, D.F., Rambo, R.F., Sansom, M.S.P., Newstead, S., Rohatgi, R., Siebold, C.

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2016-07-27
  Changes: Structure summary
• Version 1.2: 2016-08-03
  Changes: Database references
• Version 1.3: 2016-08-10
  Changes: Database references
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary