Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 327.6 kDa 
• Atom Count: 19,626 
• Modelled Residue Count: 2,503 
• Deposited Residue Count: 2,876 
• Unique protein chains: 2

 6N4Y

Metabotropic Glutamate Receptor 5 Extracellular Domain with Nb43

• PDB DOI: 10.2210/pdb6N4Y/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Lama glama
• Expression System: Trichoplusia ni, Escherichia coli BL21(DE3)
• 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., Chu, M., Weis, W.I., Mathiesen, J.M., Skiniotis, G., 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: X-RAY DIFFRACTION
• Resolution: 3.26 Å
• R-Value Free: 0.251 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

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: 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.

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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, C, D	596	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 43	E, F, G, H	123	Lama glama	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	J	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G11460AB GlyCosmos:  G11460AB GlyGen:  G11460AB

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	K	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86023QJ GlyCosmos:  G86023QJ GlyGen:  G86023QJ

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	L	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G88303DD GlyCosmos:  G88303DD GlyGen:  G88303DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	M [auth A], N [auth B], O [auth C], P [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.26 Å
• R-Value Free: 0.251 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.528	α = 90
b = 158.389	β = 101.93
c = 111.963	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
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., Chu, M., Weis, W.I., Mathiesen, J.M., Skiniotis, G., 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	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, Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary