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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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:  
    6N4Y, 6N4X, 6N50, 6N52, 6N51

  • 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 ...

    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. kobilka@stanford.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Metabotropic glutamate receptor 5A, B, C596Homo 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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody 43D [auth E]123Lama glamaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
QUS BindingDB:  6N50 Ki: min: 22, max: 1.00e+4 (nM) from 7 assay(s)
EC50: min: 150, max: 630 (nM) from 3 assay(s)
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

View Full Validation Report



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