5VBL

Structure of apelin receptor in complex with agonist peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for Apelin Control of the Human Apelin Receptor

Ma, Y.Yue, Y.Ma, Y.Zhang, Q.Zhou, Q.Song, Y.Shen, Y.Li, X.Ma, X.Li, C.Hanson, M.A.Han, G.W.Sickmier, E.A.Swaminath, G.Zhao, S.Stevens, R.C.Hu, L.A.Zhong, W.Zhang, M.Xu, F.

(2017) Structure 25: 858-866.e4

  • DOI: 10.1016/j.str.2017.04.008

  • PubMed Abstract: 
  • Apelin receptor (APJR) is a key regulator of human cardiovascular function and is activated by two different endogenous peptide ligands, apelin and Elabela, each with different isoforms diversified by length and amino acid sequence. Here we report th ...

    Apelin receptor (APJR) is a key regulator of human cardiovascular function and is activated by two different endogenous peptide ligands, apelin and Elabela, each with different isoforms diversified by length and amino acid sequence. Here we report the 2.6-Å resolution crystal structure of human APJR in complex with a designed 17-amino-acid apelin mimetic peptide agonist. The structure reveals that the peptide agonist adopts a lactam constrained curved two-site ligand binding mode. Combined with mutation analysis and molecular dynamics simulations with apelin-13 binding to the wild-type APJR, this structure provides a mechanistic understanding of apelin recognition and binding specificity. Comparison of this structure with that of other peptide receptors suggests that endogenous peptide ligands with a high degree of conformational flexibility may bind and modulate the receptors via a similar two-site binding mechanism.


    Organizational Affiliation

    Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Co., Ltd, Shanghai 201210, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
agonist peptide
A
17N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Apelin receptor,Rubredoxin,Apelin receptor Chimera
B
407Homo sapiensClostridium pasteurianum
This entity is chimeric
Mutation(s): 5 
Gene Names: APLNR (AGTRL1, APJ),
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Apelin receptor (AR) TM helix 1 in DPC micelles
Find proteins for P35414 (Homo sapiens)
Go to Gene View: APLNR
Go to UniProtKB:  P35414
Find proteins for P00268 (Clostridium pasteurianum)
Go to UniProtKB:  P00268
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
B
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
200
Query on 200
A
L-PEPTIDE LINKINGC9 H10 Cl N O2PHE
OIC
Query on OIC
A
L-PEPTIDE LINKINGC9 H15 N O2

--

ALC
Query on ALC
A
L-PEPTIDE LINKINGC9 H17 N O2ALA
NLE
Query on NLE
A
L-PEPTIDE LINKINGC6 H13 N O2LEU
HRG
Query on HRG
A
L-PEPTIDE LINKINGC7 H16 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 150.580α = 90.00
b = 44.300β = 114.87
c = 79.450γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
BUSTERrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-07-19
    Type: Database references