6OT0

Structure of human Smoothened-Gi complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-EM structure of oxysterol-bound human Smoothened coupled to a heterotrimeric Gi.

Qi, X.Liu, H.Thompson, B.McDonald, J.Zhang, C.Li, X.

(2019) Nature 571: 279-283

  • DOI: 10.1038/s41586-019-1286-0
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The oncoprotein Smoothened (SMO), a G-protein-coupled receptor (GPCR) of the Frizzled-class (class-F), transduces the Hedgehog signal from the tumour suppressor Patched-1 (PTCH1) to the glioma-associated-oncogene (GLI) transcription factors, which ac ...

    The oncoprotein Smoothened (SMO), a G-protein-coupled receptor (GPCR) of the Frizzled-class (class-F), transduces the Hedgehog signal from the tumour suppressor Patched-1 (PTCH1) to the glioma-associated-oncogene (GLI) transcription factors, which activates the Hedgehog signalling pathway 1,2 . It has remained unknown how PTCH1 modulates SMO, how SMO is stimulated to form a complex with heterotrimeric G proteins and whether G-protein coupling contributes to the activation of GLI proteins 3 . Here we show that 24,25-epoxycholesterol, which we identify as an endogenous ligand of PTCH1, can stimulate Hedgehog signalling in cells and can trigger G-protein signalling via human SMO in vitro. We present a cryo-electron microscopy structure of human SMO bound to 24(S),25-epoxycholesterol and coupled to a heterotrimeric G i protein. The structure reveals a ligand-binding site for 24(S),25-epoxycholesterol in the 7-transmembrane region, as well as a G i -coupled activation mechanism of human SMO. Notably, the G i protein presents a different arrangement from that of class-A GPCR-G i complexes. Our work provides molecular insights into Hedgehog signal transduction and the activation of a class-F GPCR.


    Organizational Affiliation

    Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA. xiaochun.li@utsouthwestern.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Smoothened homologR563Homo sapiensMutation(s): 0 
Gene Names: SMOSMOH
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Smoothened (SMO) receptor with bound oxysterol coupled to a heterotrimeric Gi
Find proteins for Q99835 (Homo sapiens)
Explore Q99835 
Go to UniProtKB:  Q99835
NIH Common Fund Data Resources
PHAROS  Q99835
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(i) subunit alpha-1A354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Smoothened (SMO) receptor with bound oxysterol coupled to a heterotrimeric Gi
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
NIH Common Fund Data Resources
PHAROS  P63096
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1B351Homo sapiensMutation(s): 0 
Gene Names: GNB1
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
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PHAROS  P62873
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2G71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Smoothened (SMO) receptor with bound oxysterol coupled to a heterotrimeric Gi
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
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PHAROS  P59768
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Fab light chainL215Mus musculusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Fab heavy chainH239Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO1
Query on CO1

Download CCD File 
R
17-[3-(3,3-DIMETHYL-OXIRANYL)-1-METHYL-PROPYL]-10,13-DIMETHYL-2,3,4,7,8,9,10,11,12,13,14,15,16,17-TETRADECAHYDRO-1H-CYC LOPENTA[A]PHENANTHREN-3-OL
C27 H44 O2
OSENKJZWYQXHBN-XVYZBDJZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-05-02 
  • Released Date: 2019-06-12 
  • Deposition Author(s): Qi, X., Li, X.

Revision History 

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-24
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Other