5VBL

Structure of apelin receptor in complex with agonist peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

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Ligand Structure Quality Assessment 


This is version 1.2 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
  • Primary Citation of Related Structures:  
    5VBL

  • 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 the 2.6-Å resolution crystal structure of human APJR in complex with a designed 17-amino-acid apelin mimetic peptide agonist ...

    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

    iHuman Institute, ShanghaiTech University, 2F Building 6, 99 Haike Road, Pudong New District, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China. Electronic address: xufei@shanghaitech.edu.cn.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
agonist peptideA17Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Apelin receptor,Rubredoxin,Apelin receptor ChimeraB407Homo sapiensClostridium pasteurianumMutation(s): 5 
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC (Subject of Investigation/LOI)
Query on OLC

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

Download Ideal Coordinates CCD File 
C [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
200
Query on 200
AL-PEPTIDE LINKINGC9 H10 Cl N O2PHE
ALC
Query on ALC
AL-PEPTIDE LINKINGC9 H17 N O2ALA
HRG
Query on HRG
AL-PEPTIDE LINKINGC7 H16 N4 O2ARG
NLE
Query on NLE
AL-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.58α = 90
b = 44.3β = 114.87
c = 79.45γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-07-19
    Changes: Database references
  • Version 1.2: 2021-06-30
    Changes: Structure summary