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 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 110.45 kDa 
• Atom Count: 7390 
• Modelled Residue Count: 904 
• Deposited Residue Count: 950 
• Unique protein chains: 1

4JKV

Structure of the human smoothened 7TM receptor in complex with an antitumor agent

• PDB DOI: 10.2210/pdb4JKV/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2013-03-11 Released: 2013-04-24 
• Deposition Author(s): Wang, C., Wu, H., Katritch, V., Han, G.W., Huang, X., Liu, W., Siu, F.Y., Roth, B.L., Cherezov, V., Stevens, R.C., GPCR Network (GPCR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.231 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 

Literature

Structure of the human smoothened receptor bound to an antitumour agent.

Wang, C., Wu, H., Katritch, V., Han, G.W., Huang, X.P., Liu, W., Siu, F.Y., Roth, B.L., Cherezov, V., Stevens, R.C.

(2013) Nature 497: 338-343

• PubMed: 23636324 
• DOI: 10.1038/nature12167
• Primary Citation of Related Structures:  
  4JKV


• PubMed Abstract: 
  

The smoothened (SMO) receptor, a key signal transducer in the hedgehog signalling pathway, is responsible for the maintenance of normal embryonic development and is implicated in carcinogenesis. It is classified as a class frizzled (class F) G-protein-coupled receptor (GPCR), although the canonical hedgehog signalling pathway involves the GLI transcription factors and the sequence similarity with class A GPCRs is less than 10%. Here we report the crystal structure of the transmembrane domain of the human SMO receptor bound to the small-molecule antagonist LY2940680 at 2.5 Å resolution. Although the SMO receptor shares the seven-transmembrane helical fold, most of the conserved motifs for class A GPCRs are absent, and the structure reveals an unusually complex arrangement of long extracellular loops stabilized by four disulphide bonds. The ligand binds at the extracellular end of the seven-transmembrane-helix bundle and forms extensive contacts with the loops.

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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
Soluble cytochrome b562, Smoothened homolog	A, B	475	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 2  Gene Names: cybC, SMO_HUMAN, SMO, SMOH 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
UniProt Groups	P0ABE7Q99835

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1KS	C [auth A], L [auth B]	4-fluoro-N-methyl-N-{1-[4-(1-methyl-1H-pyrazol-5-yl)phthalazin-1-yl]piperidin-4-yl}-2-(trifluoromethyl)benzamide C26 H24 F4 N6 O SZBGQDXLNMELTB-UHFFFAOYSA-N
OLC	D [auth A], E [auth A], F [auth A], M [auth B], N [auth B]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA	G [auth A], H [auth A], O [auth B]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PG4	K [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	J [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	I [auth A], P [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.231 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.444	α = 90
b = 98.177	β = 103.27
c = 84.293	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-03-11 
• Released Date: 2013-04-24 
Deposition Author(s): Wang, C., Wu, H., Katritch, V., Han, G.W., Huang, X., Liu, W., Siu, F.Y., Roth, B.L., Cherezov, V., Stevens, R.C., GPCR Network (GPCR)

Revision History  

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2013-05-15
  Changes: Database references
• Version 1.2: 2013-05-29
  Changes: Database references
• Version 1.3: 2013-11-27
  Changes: Structure summary
• Version 1.4: 2017-08-02
  Changes: Refinement description, Source and taxonomy
• Version 1.5: 2017-11-15
  Changes: Refinement description