9HC0 | pdb_00009hc0

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

• PDB DOI: https://doi.org/10.2210/pdb9HC0/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Tequatrovirus T4
• Expression System: Trichoplusia ni
• Mutation(s): Yes 
• Membrane Protein: Yes  MemProtMDmpstruc


• Deposited: 2024-11-08 Released: 2025-06-25 
• Deposition Author(s): 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.
• Funding Organization(s): Innosuisse, Swiss National Science Foundation, German Research Foundation (DFG)

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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

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

• PubMed: 40521617 
• DOI: https://doi.org/10.1002/pro.70104
• Primary Citation 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.

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Organizational Affiliation: 
• PSI Center for Life Sciences, Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.
Institute for Nanostructure and Solid-State Physics, Hamburg, Germany.
LeadXpro Biotech AG, Park Innovaare, Villigen PSI, Switzerland.
Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany.
PSI Center for Photon Science, Laboratory for Synchrotron Radiation and Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 51.7 kDa 
• Atom Count: 3,401 
• Modeled Residue Count: 414 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metabotropic glutamate receptor 5,Endolysin	A	444	Homo sapiens, Tequatrovirus T4	Mutation(s): 10  Gene Names: GRM5, GPRC1E, MGLUR5, E 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
UniProt Groups	P41594P00720

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4YI (Subject of Investigation/LOI)	G [auth A]	2-chloranyl-~{N}-[2-methoxy-4-[(~{E})-pyridin-2-yldiazenyl]phenyl]benzamide C19 H15 Cl N4 O2 JJRNGNCTPCWXGM-WCWDXBQESA-N
OLA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YCM	A	L-PEPTIDE LINKING	C5 H10 N2 O3 S		CYS

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 = 143.221	α = 90
b = 43.363	β = 99.86
c = 82.642	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
Innosuisse	European Union	42711.1 IP-LS
Swiss National Science Foundation	Switzerland	CRSII5_213507
Swiss National Science Foundation	Switzerland	310030_207462
German Research Foundation (DFG)	Germany	451079909

Revision History  

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