6KK7

Structure of thermal-stabilised(M6) human GLP-1 receptor transmembrane domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Mutagenesis facilitated crystallization of GLP-1R.

Xu, Y.Wang, Y.Wang, Y.Liu, K.Peng, Y.Yao, D.Tao, H.Liu, H.Song, G.

(2019) IUCrJ 6: 996-1006

  • DOI: 10.1107/S2052252519013496
  • Primary Citation of Related Structures:  
    6KK1, 6KJV, 6KK7

  • PubMed Abstract: 
  • The class B family of G-protein-coupled receptors (GPCRs) has long been a paradigm for peptide hormone recognition and signal transduction. One class B GPCR, the glucagon-like peptide-1 receptor (GLP-1R), has been considered as an anti-diabetes drug target and there are several peptidic drugs available for the treatment of this overwhelming disease ...

    The class B family of G-protein-coupled receptors (GPCRs) has long been a paradigm for peptide hormone recognition and signal transduction. One class B GPCR, the glucagon-like peptide-1 receptor (GLP-1R), has been considered as an anti-diabetes drug target and there are several peptidic drugs available for the treatment of this overwhelming disease. The previously determined structures of inactive GLP-1R in complex with two negative allosteric modulators include ten thermal-stabilizing mutations that were selected from a total of 98 designed mutations. Here we systematically summarize all 98 mutations we have tested and the results suggest that the mutagenesis strategy that strengthens inter-helical hydro-phobic interactions shows the highest success rate. We further investigate four back mutations by thermal-shift assay, crystallization and molecular dynamic simulations, and conclude that mutation I196 2.66b F increases thermal stability intrinsically and that mutation S271 4.47b A decreases crystal packing entropy extrinsically, while mutations S193 2.63b C and M233 3.36b C may be dispensable since these two cysteines are not di-sulfide-linked. Our results indicate intrinsic connections between different regions of GPCR transmembrane helices and the current data suggest a general mutagenesis principle for structural determination of GPCRs and other membrane proteins.


    Organizational Affiliation

    Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucagon-like peptide 1 receptor,Endolysin,Glucagon-like peptide 1 receptorA, B455Homo sapiensEscherichia virus T4Mutation(s): 10 
Gene Names: GLP1RE
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P43220 (Homo sapiens)
Explore P43220 
Go to UniProtKB:  P43220
PHAROS:  P43220
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
97Y (Subject of Investigation/LOI)
Query on 97Y

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]N-{4-[(R)-(3,3-dimethylcyclobutyl)({6-[4-(trifluoromethyl)-1H-imidazol-1-yl]pyridin-3-yl}amino)methyl]benzene-1-carbonyl}-beta-alanine
C26 H28 F3 N5 O3
MYZIDYJMNWEJMC-QHCPKHFHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.23α = 92.48
b = 71.06β = 92.61
c = 81γ = 105.1
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2019-07-23 
  • Released Date: 2019-11-13 
  • Deposition Author(s): Song, G.

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references, Structure summary