6KNM

Apelin receptor in complex with single domain antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-guided discovery of a single-domain antibody agonist against human apelin receptor.

Ma, Y.Ding, Y.Song, X.Ma, X.Li, X.Zhang, N.Song, Y.Sun, Y.Shen, Y.Zhong, W.Hu, L.A.Ma, Y.Zhang, M.Y.

(2020) Sci Adv 6: eaax7379-eaax7379

  • DOI: 10.1126/sciadv.aax7379

  • PubMed Abstract: 
  • Developing antibody agonists targeting the human apelin receptor (APJ) is a promising therapeutic approach for the treatment of chronic heart failure. Here, we report the structure-guided discovery of a single-domain antibody (sdAb) agonist JN241-9, ...

    Developing antibody agonists targeting the human apelin receptor (APJ) is a promising therapeutic approach for the treatment of chronic heart failure. Here, we report the structure-guided discovery of a single-domain antibody (sdAb) agonist JN241-9, based on the cocrystal structure of APJ with an sdAb antagonist JN241, the first cocrystal structure of a class A G protein-coupled receptor (GPCR) with a functional antibody. As revealed by the structure, JN241 binds to the extracellular side of APJ, makes critical contacts with the second extracellular loop, and inserts the CDR3 into the ligand-binding pocket. We converted JN241 into a full agonist JN241-9 by inserting a tyrosine into the CDR3. Modeling and molecular dynamics simulation shed light on JN241-9-stimulated receptor activation, providing structural insights for finding agonistic antibodies against class A GPCRs.


    Organizational Affiliation

    Therapeutic Discovery, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,Amgen Discovery Research, Amgen Asia R&D Center, Amgen Biopharmaceutical R&D (Shanghai) Co. Ltd., 13th Floor, Building No. 2, 4560 Jinke Road, Zhangjiang, Shanghai 201210, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apelin receptor,Rubredoxin,Apelin receptor
B
407Homo sapiensClostridium pasteurianum
This entity is chimeric
Mutation(s): 5 
Gene Names: APLNR (AGTRL1, APJ),
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Single domain antibody JN241
A
129N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.258 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.780α = 90.00
b = 48.390β = 90.00
c = 350.100γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-02-12
    Type: Advisory, Database references