Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 198.37 kDa 
• Atom Count: 7,736 
• Modelled Residue Count: 993 
• Deposited Residue Count: 1,754 
• Unique protein chains: 1

 6N4X

Metabotropic Glutamate Receptor 5 Apo Form Ligand Binding Domain

• PDB DOI:  https://doi.org/10.2210/pdb6N4X/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2018-11-20 Released: 2019-01-23 
• Deposition Author(s): Koehl, A., Hu, H., Feng, D., Sun, B., Weis, W.I., Skiniotis, G.S., Mathiesen, J.M., Kobilka, B.K.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.282 
• R-Value Work: 0.270 
• R-Value Observed: 0.271 

Literature

Structural insights into the activation of metabotropic glutamate receptors.

Koehl, A., Hu, H., Feng, D., Sun, B., Zhang, Y., Robertson, M.J., Chu, M., Kobilka, T.S., Laermans, T., Steyaert, J., Tarrasch, J., Dutta, S., Fonseca, R., Weis, W.I., Mathiesen, J.M., Skiniotis, G., Kobilka, B.K.

(2019) Nature 566: 79-84

• PubMed: 30675062 
• DOI: https://doi.org/10.1038/s41586-019-0881-4
• Primary Citation of Related Structures:  
  6N4X, 6N4Y, 6N50, 6N51, 6N52


• PubMed Abstract: 
  

Metabotropic glutamate receptors are family C G-protein-coupled receptors. They form obligate dimers and possess extracellular ligand-binding Venus flytrap domains, which are linked by cysteine-rich domains to their 7-transmembrane domains. Spectroscopic studies show that signalling is a dynamic process, in which large-scale conformational changes underlie the transmission of signals from the extracellular Venus flytraps to the G protein-coupling domains-the 7-transmembrane domains-in the membrane. Here, using a combination of X-ray crystallography, cryo-electron microscopy and signalling studies, we present a structural framework for the activation mechanism of metabotropic glutamate receptor subtype 5. Our results show that agonist binding at the Venus flytraps leads to a compaction of the intersubunit dimer interface, thereby bringing the cysteine-rich domains into close proximity. Interactions between the cysteine-rich domains and the second extracellular loops of the receptor enable the rigid-body repositioning of the 7-transmembrane domains, which come into contact with each other to initiate signalling.

---

Organizational Affiliation: 

ConfometRx, Santa Clara, CA, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metabotropic glutamate receptor 5	A, B	877	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG	G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.282 
• R-Value Work: 0.270 
• R-Value Observed: 0.271 
• Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.084	α = 90
b = 174.1	β = 90
c = 180.902	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Koehl, A., Hu, H., Feng, D., Sun, B., Weis, W.I., Skiniotis, G.S., Mathiesen, J.M., Kobilka, B.K.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS092695
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS028471

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2019-02-06
  Changes: Data collection, Database references
• Version 1.2: 2019-02-20
  Changes: Data collection, Database references
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary