2.9A XFEL structure of the multi-domain human smoothened receptor (with E194M mutation) in complex with TC114

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

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This is version 1.4 of the entry. See complete history


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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Smoothened homolog,Flavodoxin,Smoothened homolog
A, B
653Homo sapiensNitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 3 
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
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.59α = 90
b = 349.54β = 101.1
c = 61.76γ = 90
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

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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: 2019-11-20
    Changes: Data collection
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary