7SUS

Crystal structure of Apelin receptor in complex with small molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41594-022-00797-5
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apelin receptor, with Rubredoxin insertion407Homo sapiensClostridium pasteurianumMutation(s): 7 
Gene Names: APLNRAGTRL1APJ
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00268P35414
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8EH (Subject of Investigation/LOI)
Query on 8EH

Download Ideal Coordinates CCD File 
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
Query on OLC

Download Ideal Coordinates CCD File 
D [auth A](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.01α = 90
b = 44.56β = 115.62
c = 79.68γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

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