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 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 836Click on this verticalbar to view detailsBest fitted FMNClick on this verticalbar to view detailsBest fitted OLCClick on this verticalbar to view details

This is version 1.3 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: https://doi.org/10.1038/ncomms15383
  • Primary Citation of Related Structures:  
    5V56, 5V57

  • 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, 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

    iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Smoothened homolog,Flavodoxin,Smoothened homolog
A, B
648Homo sapiensNitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 2 
Gene Names: SMOSMOHDVU_2680
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P00323 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P00323 
Go to UniProtKB:  P00323
Find proteins for Q99835 (Homo sapiens)
Explore Q99835 
Go to UniProtKB:  Q99835
PHAROS:  Q99835
GTEx:  ENSG00000128602 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00323Q99835
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.240 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
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



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 836Click on this verticalbar to view detailsBest fitted FMNClick on this verticalbar to view detailsBest fitted OLCClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary