5V57

3.0A SYN structure of the multi-domain human smoothened receptor in complex with TC114


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand.

Zhang, X.Zhao, F.Wu, Y.Yang, J.Han, G.W.Zhao, S.Ishchenko, A.Ye, L.Lin, X.Ding, K.Dharmarajan, V.Griffin, P.R.Gati, C.Nelson, G.Hunter, M.S.Hanson, M.A.Cherezov, V.Stevens, R.C.Tan, W.Tao, H.Xu, F.

(2017) Nat Commun 8: 15383-15383

  • DOI: 10.1038/ncomms15383
  • Primary Citation of Related Structures:  
    5V57, 5V56

  • PubMed Abstract: 
  • The Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bou ...

    The Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combining the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.


    Organizational Affiliation

    School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Smoothened homolog,Flavodoxin,Smoothened homologAB648Homo sapiensDesulfovibrio vulgaris str. HildenboroughMutation(s): 2 
Gene Names: SMOSMOH
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class F
Protein: 
Smoothened (SMO) receptor (multi-domain) in complex with TC114
Find proteins for P00323 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Explore P00323 
Go to UniProtKB:  P00323
Find proteins for Q99835 (Homo sapiens)
Explore Q99835 
Go to UniProtKB:  Q99835
NIH Common Fund Data Resources
PHAROS  Q99835
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
836
Query on 836

Download CCD File 
A, B
N-methyl-N-[1-[4-(2-methylpyrazol-3-yl)phthalazin-1-yl]piperidin-4-yl]-4-nitro-2-(trifluoromethyl)benzamide
C26 H24 F3 N7 O3
ZDEZQXNVPSUJHK-UHFFFAOYSA-N
 Ligand Interaction
FMN
Query on FMN

Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
OLC
Query on OLC

Download CCD File 
B
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.08α = 90
b = 356.36β = 102.79
c = 59.09γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Database references