8T7H | pdb_00008t7h

Quis-bound intermediate mGlu5

• PDB DOI: https://doi.org/10.2210/pdb8T7H/pdb
• EM Map EMD-41092: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Lama glama
• Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2023-06-20 Released: 2023-10-11 
• Deposition Author(s): Krishna Kumar, K., Wang, H., Kobilka, B.K.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Stepwise activation of a metabotropic glutamate receptor.

Krishna Kumar, K., Wang, H., Habrian, C., Latorraca, N.R., Xu, J., O'Brien, E.S., Zhang, C., Montabana, E., Koehl, A., Marqusee, S., Isacoff, E.Y., Kobilka, B.K.

(2024) Nature 629: 951-956

• PubMed: 38632403 
• DOI: https://doi.org/10.1038/s41586-024-07327-x
• Primary Citation Related Structures: 
  8T6J, 8T7H, 8T8M, 8TAO


• PubMed Abstract: 
  

  Metabotropic glutamate receptors belong to a family of G protein-coupled receptors that are obligate dimers and possess a large extracellular ligand-binding domain that is linked via a cysteine-rich domain to their 7-transmembrane domain ¹ . Upon activation, these receptors undergo a large conformational change to transmit the ligand binding signal from the extracellular ligand-binding domain to the G protein-coupling 7-transmembrane domain ² . In this manuscript, we propose a model for a sequential, multistep activation mechanism of metabotropic glutamate receptor subtype 5. We present a series of structures in lipid nanodiscs, from inactive to fully active, including agonist-bound intermediate states. Further, using bulk and single-molecule fluorescence imaging, we reveal distinct receptor conformations upon allosteric modulator and G protein binding.

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Organizational Affiliation: 
• Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA.
QB3 Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 224.82 kDa 
• Atom Count: 13,100 
• Modeled Residue Count: 1,794 
• Deposited Residue Count: 2,008 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metabotropic glutamate receptor 5	A, B	881	Homo sapiens	Mutation(s): 0  Gene Names: GRM5, GPRC1E, MGLUR5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P41594 (Homo sapiens) Explore P41594  Go to UniProtKB:  P41594
PHAROS:  P41594 GTEx:  ENSG00000168959

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 43	C, D	123	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QUS (Subject of Investigation/LOI)	E [auth A], F [auth B]	(S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID C5 H7 N3 O5 ASNFTDCKZKHJSW-REOHCLBHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
QUS	BindingDB:  8T7H	Ki: min: 1.00e+4, max: 1.00e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-11 
Deposition Author(s): Krishna Kumar, K., Wang, H., Kobilka, B.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS028471

Revision History  

• Version 1.0: 2023-10-11
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Database references
• Version 1.2: 2024-06-05
  Changes: Database references
• Version 1.3: 2024-10-23
  Changes: Data collection, Structure summary
• Version 1.4: 2025-05-14
  Changes: Data collection