6KJV | pdb_00006kjv

Structure of thermal-stabilised(M9) human GLP-1 receptor transmembrane domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.280 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.247 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.249 (Depositor) 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1107/S2052252519013496
  • Primary Citation of Related Structures:  
    6KJV, 6KK1, 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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucagon-like peptide 1 receptor,Endolysin,Glucagon-like peptide 1 receptor
A, B
455Homo sapiensTequatrovirus T4Mutation(s): 13 
Gene Names: GLP1R
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for P43220 (Homo sapiens)
Explore P43220 
Go to UniProtKB:  P43220
PHAROS:  P43220
GTEx:  ENSG00000112164 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P43220
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.247 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.249 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.03α = 91.53
b = 68.3β = 90.34
c = 83.43γ = 106.49
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • 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
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary