Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 53.73 kDa 
• Atom Count: 3237 
• Residue Count: 411 
• Unique protein chains: 1

5KW2

The extra-helical binding site of GPR40 and the structural basis for allosteric agonism and incretin stimulation

• DOI: 10.2210/pdb5KW2/pdb

• Classification: Fatty acid binding protein/Hydrolase
• Organism(s): Homo sapiens, Escherichia virus T4
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): Yes 


• Deposited: 2016-07-15 Released: 2018-05-02 
• Deposition Author(s): Ho, J.D., Chau, B., Rodgers, L., Lu, F., Wilbur, K.L., Otto, K.A., Chen, Y., Song, M., Riley, J.P., Yang, H.-C., Reynolds, N.A., Kahl, S.D., Lewis, A.P., Groshong, C., Madsen, R.E., Conners, K., Linswala, J.P., Gheyi, T., Saflor, M.D., Lee, M.R., Benach, J., Baker, K.A., Montrose-Rafizadeh, C., Genin, M.J., Miller, A.R., Hamdouchi, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 0.273 
• R-Value Work: 0.230 
• R-Value Observed: 0.233 

Literature

Structural basis for GPR40 allosteric agonism and incretin stimulation.

Ho, J.D., Chau, B., Rodgers, L., Lu, F., Wilbur, K.L., Otto, K.A., Chen, Y., Song, M., Riley, J.P., Yang, H.C., Reynolds, N.A., Kahl, S.D., Lewis, A.P., Groshong, C., Madsen, R.E., Conners, K., Lineswala, J.P., Gheyi, T., Saflor, M.D., Lee, M.R., Benach, J., Baker, K.A., Montrose-Rafizadeh, C., Genin, M.J., Miller, A.R., Hamdouchi, C.

(2018) Nat Commun 9: 1645-1645

• PubMed: 29695780 
• DOI: 10.1038/s41467-017-01240-w
• Primary Citation of Related Structures:  
  5KW2


• PubMed Abstract: 
  

Activation of free fatty acid receptor 1 (GPR40) by synthetic partial and full agonists occur via distinct allosteric sites. A crystal structure of GPR40-TAK-875 complex revealed the allosteric site for the partial agonist. Here we report the 2.76-Å crystal structure of human GPR40 in complex with a synthetic full agonist, compound 1, bound to the second allosteric site. Unlike TAK-875, which acts as a Gα _q -coupled partial agonist, compound 1 is a dual Gα _q and Gα _s -coupled full agonist. compound 1 binds in the lipid-rich region of the receptor near intracellular loop 2 (ICL2), in which the stabilization of ICL2 by the ligand is likely the primary mechanism for the enhanced G protein activities. The endogenous free fatty acid (FFA), γ-linolenic acid, can be computationally modeled in this site. Both γ-linolenic acid and compound 1 exhibit positive cooperativity with TAK-875, suggesting that this site could also serve as a FFA binding site.

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Organizational Affiliation: 

Lilly Research Laboratories, Lilly Corporate Center, 355 East Merrill Street, Indianapolis, IN, 46285, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Free fatty acid receptor 1,Lysozyme,Free fatty acid receptor 1	A	491	Homo sapiens, Escherichia virus T4	Mutation(s): 6  Gene Names: FFAR1, GPR40 EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
Find proteins for O14842 (Homo sapiens) Explore O14842  Go to UniProtKB:  O14842
NIH Common Fund Data Resources
PHAROS  O14842 GTEx  ENSG00000126266

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6XQ	A	(3~{S})-3-cyclopropyl-3-[2-[1-[2-[2,2-dimethylpropyl-(6-methylpyridin-2-yl)carbamoyl]-5-methoxy-phenyl]piperidin-4-yl]-1-benzofuran-6-yl]propanoic acid C38 H45 N3 O5 RJZJYKXHTPUHAO-HKBQPEDESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 0.273 
• R-Value Work: 0.230 
• R-Value Observed: 0.233 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.654	α = 90
b = 55.95	β = 93.77
c = 80.313	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-07-15 
• Released Date: 2018-05-02 
Deposition Author(s): Ho, J.D., Chau, B., Rodgers, L., Lu, F., Wilbur, K.L., Otto, K.A., Chen, Y., Song, M., Riley, J.P., Yang, H.-C., Reynolds, N.A., Kahl, S.D., Lewis, A.P., Groshong, C., Madsen, R.E., Conners, K., Linswala, J.P., Gheyi, T., Saflor, M.D., Lee, M.R., Benach, J., Baker, K.A., Montrose-Rafizadeh, C., Genin, M.J., Miller, A.R., Hamdouchi, C.

Revision History 

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2018-05-09
  Changes: Data collection, Database references