Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55441.47 
• Atom Count: 3699 
• Residue Count: 475 
• Unique protein chains: 1

4N4W

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

• DOI: 10.2210/pdb4N4W/pdb

• Classification: Membrane Protein Transport Protein
• Organism(s): Homo sapiens, Shigella flexneri serotype 5b (strain 8401)
• Expression System: Spodoptera frugiperda
• Mutation(s): 3 


• 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: 2.8 Å
• R-Value Free: 0.253 
• R-Value Work: 0.204 

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:  
  4QIN, 4QIM


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cytochrome b(562),Smoothened homolog	A	475	Homo sapiens, Shigella flexneri serotype 5b (strain 8401) This entity is chimeric	Mutation(s): 3  Gene Names: SMO (SMOH), cybC
Find proteins for Q99835 (Homo sapiens) Go to Gene View: SMO Go to UniProtKB:  Q99835
Find proteins for Q0SXH8 (Shigella flexneri serotype 5b (strain 8401)) Go to UniProtKB:  Q0SXH8

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
OLC	A	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate 1-Oleoyl-R-glycerol C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SNT	A	(E)-N-(4-benzylpiperazin-1-yl)-1-(3,5-dimethyl-1-phenyl-1H-pyrazol-4-yl)methanimine SANT-1 C23 H27 N5 FOORCIAZMIWALX-JJIBRWJFSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
PG4	A	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	A	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SNT	IC50: 4.7 - 25 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.253 
• R-Value Work: 0.204 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 84.640	α = 90.00
b = 110.880	β = 90.00
c = 145.210	γ = 90.00

Software Package:

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

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
  Type: Database references
• Version 1.2: 2017-06-07
  Type: Database references, Structure summary
• Version 1.3: 2017-11-15
  Type: Refinement description