5NX2 | pdb_00005nx2

Crystal structure of thermostabilised full-length GLP-1R in complex with a truncated peptide agonist at 3.7 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5NX2/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2017-05-09 Released: 2017-06-14 
• Deposition Author(s): Rappas, M., Jazayeri, A., Brown, A.J.H., Kean, J., Errey, J.C., Robertson, N., Fiez-Vandal, C., Andrews, S.P., Congreve, M., Bortolato, A., Mason, J.S., Baig, A.H., Teobald, I., Dore, A.S., Weir, M., Cooke, R.M., Marshall, F.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 
  0.334 (Depositor), 0.347 (DCC) 
• R-Value Work: 
  0.285 (Depositor), 0.301 (DCC) 
• R-Value Observed: 
  0.287 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of the GLP-1 receptor bound to a peptide agonist.

Jazayeri, A., Rappas, M., Brown, A.J.H., Kean, J., Errey, J.C., Robertson, N.J., Fiez-Vandal, C., Andrews, S.P., Congreve, M., Bortolato, A., Mason, J.S., Baig, A.H., Teobald, I., Dore, A.S., Weir, M., Cooke, R.M., Marshall, F.H.

(2017) Nature 546: 254-258

• PubMed: 28562585 
• DOI: https://doi.org/10.1038/nature22800
• Primary Citation Related Structures: 
  5NX2


• PubMed Abstract: 
  

  Glucagon-like peptide 1 (GLP-1) regulates glucose homeostasis through the control of insulin release from the pancreas. GLP-1 peptide agonists are efficacious drugs for the treatment of diabetes. To gain insight into the molecular mechanism of action of GLP-1 peptides, here we report the crystal structure of the full-length GLP-1 receptor bound to a truncated peptide agonist. The peptide agonist retains an α-helical conformation as it sits deep within the receptor-binding pocket. The arrangement of the transmembrane helices reveals hallmarks of an active conformation similar to that observed in class A receptors. Guided by this structural information, we design peptide agonists with potent in vivo activity in a mouse model of diabetes.

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Organizational Affiliation: 
• Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.09 kDa 
• Atom Count: 3,410 
• Modeled Residue Count: 399 
• Deposited Residue Count: 432 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucagon-like peptide 1 receptor	A	422	Homo sapiens	Mutation(s): 12  Gene Names: GLP1R Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P43220 (Homo sapiens) Explore P43220  Go to UniProtKB:  P43220
PHAROS:  P43220 GTEx:  ENSG00000112164
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P43220-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
truncated peptide agonist	B	10	synthetic construct	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SOG	E [auth A], F [auth A], G [auth A]	octyl 1-thio-beta-D-glucopyranoside C14 H28 O5 S CGVLVOOFCGWBCS-RGDJUOJXSA-N
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
9DT	B	L-PEPTIDE LINKING	C10 H12 F N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free:  0.334 (Depositor), 0.347 (DCC) 
• R-Value Work:  0.285 (Depositor), 0.301 (DCC) 
• R-Value Observed: 0.287 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.435	α = 90
b = 94.435	β = 90
c = 163.905	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Rappas, M., Jazayeri, A., Brown, A.J.H., Kean, J., Errey, J.C., Robertson, N., Fiez-Vandal, C., Andrews, S.P., Congreve, M., Bortolato, A., Mason, J.S., Baig, A.H., Teobald, I., Dore, A.S., Weir, M., Cooke, R.M., Marshall, F.H.

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 3.1: 2024-01-17
  Changes: Refinement description