Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.39 kDa 
• Atom Count: 3707 
• Modelled Residue Count: 457 
• Deposited Residue Count: 475 
• Unique protein chains: 1

4N4W

Structure of the human smoothened receptor in complex with SANT-1.

• PDB DOI: 10.2210/pdb4N4W/pdb

• Classification: Membrane Protein, Transport Protein
• Organism(s): Shigella flexneri 5 str. 8401, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2013-10-08 Released: 2014-01-22 
• Deposition Author(s): Wang, C., Wu, H., Han, G.W., Cherezov, V., Stevens, R.C., GPCR Network (GPCR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.253 
• R-Value Work: 0.204 
• R-Value Observed: 0.207 

Literature

Structural basis for Smoothened receptor modulation and chemoresistance to anticancer drugs.

Wang, C., Wu, H., Evron, T., Vardy, E., Han, G.W., Huang, X.P., Hufeisen, S.J., Mangano, T.J., Urban, D.J., Katritch, V., Cherezov, V., Caron, M.G., Roth, B.L., Stevens, R.C.

(2014) Nat Commun 5: 4355-4355

• PubMed: 25008467 
• DOI: 10.1038/ncomms5355
• Primary Citation of Related Structures:  
  4N4W, 4QIM, 4QIN


• PubMed Abstract: 
  

The Smoothened receptor (SMO) mediates signal transduction in the hedgehog pathway, which is implicated in normal development and carcinogenesis. SMO antagonists can suppress the growth of some tumours; however, mutations at SMO have been found to abolish their antitumour effects, a phenomenon known as chemoresistance. Here we report three crystal structures of human SMO bound to the antagonists SANT1 and Anta XV, and the agonist, SAG1.5, at 2.6-2.8 Å resolution. The long and narrow cavity in the transmembrane domain of SMO harbours multiple ligand binding sites, where SANT1 binds at a deeper site as compared with other ligands. Distinct interactions at D473(6.54f) elucidated the structural basis for the differential effects of chemoresistance mutations on SMO antagonists. The agonist SAG1.5 induces a conformational rearrangement of the binding pocket residues, which could contribute to SMO activation. Collectively, these studies reveal the structural basis for the modulation of SMO by small molecules.

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Organizational Affiliation: 

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b(562),Smoothened homolog	A	475	Shigella flexneri 5 str. 8401, Homo sapiens This entity is chimeric	Mutation(s): 3  Gene Names: cybC, SFV_4255, SMO, SMOH Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q0SXH8 (Shigella flexneri serotype 5b (strain 8401)) Explore Q0SXH8  Go to UniProtKB:  Q0SXH8
Find proteins for Q99835 (Homo sapiens) Explore Q99835  Go to UniProtKB:  Q99835
PHAROS:  Q99835
UniProt Groups	Q0SXH8Q99835

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N/A
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SNT	C [auth A]	(E)-N-(4-benzylpiperazin-1-yl)-1-(3,5-dimethyl-1-phenyl-1H-pyrazol-4-yl)methanimine C23 H27 N5 FOORCIAZMIWALX-JJIBRWJFSA-N
OLC	F [auth A], G [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
PG4	I [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SNT	BindingDB:  4N4W	IC50: min: 4.7, max: 25 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.253 
• R-Value Work: 0.204 
• R-Value Observed: 0.207 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.64	α = 90
b = 110.88	β = 90
c = 145.21	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-10-08 
• Released Date: 2014-01-22 
Deposition Author(s): Wang, C., Wu, H., Han, G.W., Cherezov, V., Stevens, R.C., GPCR Network (GPCR)

Revision History  

• Version 1.0: 2014-01-22
  Type: Initial release
  
• Version 1.1: 2014-07-30
  Changes: Database references
• Version 1.2: 2017-06-07
  Changes: Database references, Structure summary
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary