9HC0 | pdb_00009hc0

Dark structure of the human metabotropic glutamate receptor 5 transmembrane domain bound to photoswitchable ligand alloswitch-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 
    0.271 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Apo-state structure of the metabotropic glutamate receptor 5 transmembrane domain obtained using a photoswitchable ligand.

Kondo, Y.Hatton, C.Cheng, R.Trabuco, M.Glover, H.Bertrand, Q.Stierli, F.Seidel, H.P.Mason, T.Sarma, S.Tellkamp, F.Kepa, M.Dworkowski, F.Mehrabi, P.Hennig, M.Standfuss, J.

(2025) Protein Sci 34: e70104-e70104

  • DOI: https://doi.org/10.1002/pro.70104
  • Primary Citation of Related Structures:  
    9HC0, 9HC3

  • PubMed Abstract: 

    Metabotropic glutamate receptor 5 (mGlu5) is implicated in various neurodegenerative disorders, making it an attractive drug target. Although several ligand-bound crystal structures of mGlu5 exist, their apo-state crystal structure remains unknown. Here, we study mGlu5 structural changes using the photochemical affinity switch, alloswitch-1, in combination with time-resolved freeze-trapping methods. By X-ray crystallography, we demonstrated that isomerizing alloswitch-1 leads to its release from the binding pocket within a few seconds. The apo structure, determined at a resolution of 2.9 Å, is more comparable to the inactive state than to the active state. Our approach presents an accessible alternative to time-resolved serial crystallography for capturing thermodynamically stable transient intermediates. The mGlu5 apo-structure provides molecular insights into the ligand-free allosteric pocket, which can guide the design of new allosteric modulators.


  • Organizational Affiliation
    • PSI Center for Life Sciences, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metabotropic glutamate receptor 5,Endolysin444Homo sapiensTequatrovirus T4Mutation(s): 10 
Gene Names: GRM5GPRC1EMGLUR5E
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for P41594 (Homo sapiens)
Explore P41594 
Go to UniProtKB:  P41594
PHAROS:  P41594
GTEx:  ENSG00000168959 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP41594P00720
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free:  0.271 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.221α = 90
b = 43.363β = 99.86
c = 82.642γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
InnosuisseEuropean Union42711.1 IP-LS
Swiss National Science FoundationSwitzerlandCRSII5_213507
Swiss National Science FoundationSwitzerland310030_207462
German Research Foundation (DFG)Germany451079909

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release