7SUS | pdb_00007sus

Crystal structure of Apelin receptor in complex with small molecule

• PDB DOI: https://doi.org/10.2210/pdb7SUS/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Clostridium pasteurianum
• Expression System: Trichoplusia ni
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2021-11-18 Released: 2022-07-27 
• Deposition Author(s): Xu, F., Yue, Y., Liu, L.E., Han, G.W., Hanson, M.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.274 (Depositor), 0.342 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.302 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Starting Models: experimental

Literature

Structural insight into apelin receptor-G protein stoichiometry.

Yue, Y., Liu, L., Wu, L.J., Wu, Y., Wang, L., Li, F., Liu, J., Han, G.W., Chen, B., Lin, X., Brouillette, R.L., Breault, E., Longpre, J.M., Shi, S., Lei, H., Sarret, P., Stevens, R.C., Hanson, M.A., Xu, F.

(2022) Nat Struct Mol Biol 29: 688-697

• PubMed: 35817871 
• DOI: https://doi.org/10.1038/s41594-022-00797-5
• Primary Citation Related Structures: 
  7SUS, 7W0L, 7W0M, 7W0N, 7W0O, 7W0P


• PubMed Abstract: 
  

  The technique of cryogenic-electron microscopy (cryo-EM) has revolutionized the field of membrane protein structure and function with a focus on the dominantly observed molecular species. This report describes the structural characterization of a fully active human apelin receptor (APJR) complexed with heterotrimeric G protein observed in both 2:1 and 1:1 stoichiometric ratios. We use cryo-EM single-particle analysis to determine the structural details of both species from the same sample preparation. Protein preparations, in the presence of the endogenous peptide ligand ELA or a synthetic small molecule, both demonstrate these mixed stoichiometric states. Structural differences in G protein engagement between dimeric and monomeric APJR suggest a role for the stoichiometry of G protein-coupled receptor- (GPCR-)G protein coupling on downstream signaling and receptor pharmacology. Furthermore, a small, hydrophobic dimer interface provides a starting framework for additional class A GPCR dimerization studies. Together, these findings uncover a mechanism of versatile regulation through oligomerization by which GPCRs can modulate their signaling.

---

Organizational Affiliation: 
• iHuman Institute, ShanghaiTech University, Shanghai, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China.
Departments of Biological Sciences and Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, USA.
Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institute of Pharmacology at Sherbrooke, University of Sherbrooke, Sherbrooke, Quebec, Canada.
Structure Therapeutics, South San Francisco, CA, USA.
iHuman Institute, ShanghaiTech University, Shanghai, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 47.38 kDa 
• Atom Count: 2,738 
• Modeled Residue Count: 347 
• Deposited Residue Count: 407 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apelin receptor, with Rubredoxin insertion	A	407	Homo sapiens, Clostridium pasteurianum	Mutation(s): 7  Gene Names: APLNR, AGTRL1, APJ Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P00268 (Clostridium pasteurianum) Explore P00268  Go to UniProtKB:  P00268
Find proteins for P35414 (Homo sapiens) Explore P35414  Go to UniProtKB:  P35414
PHAROS:  P35414 GTEx:  ENSG00000134817
UniProt Groups	P00268P35414

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8EH (Subject of Investigation/LOI)	C [auth A]	(1R,2S)-N-[4-(2,6-dimethoxyphenyl)-5-(6-methylpyridin-2-yl)-1,2,4-triazol-3-yl]-1-(5-methylpyrimidin-2-yl)-1-oxidanyl-propane-2-sulfonamide C24 H27 N7 O5 S HNGYVRSMVVCWGF-KKSFZXQISA-N
OLC	D [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.274 (Depositor), 0.342 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.302 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.01	α = 90
b = 44.56	β = 115.62
c = 79.68	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-07-27 
Deposition Author(s): Xu, F., Yue, Y., Liu, L.E., Han, G.W., Hanson, M.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary