5V56

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.218 

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:  

  • 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

    Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,GPCR Consortium, San Marcos, California 92078, USA.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Medical Research Council, Laboratory of Molecular Biology, Cambridge, Biomedical Campus, Francis Crick Avenue, Cambridge CB2 OQH, UK.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.,University of Chinese Academy of Sciences, Beijing 100049, China.,Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, USA.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China.,Shanghai Institute of Materia Medica, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 555 Zuchongzhi Lu, Building 3, Room 426, Shanghai 201203, China.,Departments of Chemistry, Biological Sciences and Physics &Astronomy, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.,Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.,iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Smoothened homolog,Flavodoxin,Smoothened homolog
A, B
653Homo sapiensDesulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)
This entity is chimeric
Mutation(s): 3 
Gene Names: SMO (SMOH),
Find proteins for Q99835 (Homo sapiens)
Go to Gene View: SMO
Go to UniProtKB:  Q99835
Find proteins for P00323 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  P00323
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
836
Query on 836

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

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.590α = 90.00
b = 349.540β = 101.10
c = 61.760γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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