6N50

Metabotropic Glutamate Receptor 5 Extracellular Domain in Complex with Nb43 and L-quisqualic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.75 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.268 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


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

  • 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

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metabotropic glutamate receptor 5
A, B, C
596Homo sapiensMutation(s): 0 
Gene Names: GRM5GPRC1EMGLUR5
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41594
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P41594-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 43D [auth E]123Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H [auth B],
J [auth C],
K [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
QUS
Query on QUS

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
L [auth C]
(S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID
C5 H7 N3 O5
ASNFTDCKZKHJSW-REOHCLBHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.75 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.268 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.433α = 90
b = 157.159β = 90
c = 208.112γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS092695
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS028471

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.6: 2024-10-23
    Changes: Structure summary