6N4X

Metabotropic Glutamate Receptor 5 Apo Form Ligand Binding Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.270 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/s41586-019-0881-4
  • Primary Citation of Related Structures:  

  • 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. Spectrosc ...

    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

    Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,ConfometRx, Santa Clara, CA, USA. kobilka@stanford.edu.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.,Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. jmm@sund.ku.dk.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. kobilka@stanford.edu.,ConfometRx, Santa Clara, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. yiorgo@stanford.edu.,Life Sciences Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. yiorgo@stanford.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metabotropic glutamate receptor 5
A, B
877Homo sapiensMutation(s): 0 
Gene Names: GRM5 (GPRC1E, MGLUR5)
Find proteins for P41594 (Homo sapiens)
Go to Gene View: GRM5
Go to UniProtKB:  P41594
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.270 
  • Space Group: P 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 119.084α = 90.00
b = 174.100β = 90.00
c = 180.902γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited StatesNS092695
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited StatesNS028471

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-02-06
    Type: Data collection, Database references
  • Version 1.2: 2019-02-20
    Type: Data collection, Database references