6KNM | pdb_00006knm

Apelin receptor in complex with single domain antibody

• PDB DOI: https://doi.org/10.2210/pdb6KNM/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Clostridium pasteurianum, Camelus bactrianus
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2019-08-06 Released: 2020-01-29 
• Deposition Author(s): Ma, Y.B., Ding, Y., Song, X., Ma, X., Li, X., Zhang, N., Song, Y., Sun, Y., Shen, Y., Zhong, W., Hu, L.A., Ma, Y.L., Zhang, M.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.305 (Depositor), 0.312 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.261 (DCC) 
• R-Value Observed: 
  0.260 (Depositor) 

Starting Models: experimental

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

• PubMed: 31998837 
• DOI: https://doi.org/10.1126/sciadv.aax7379
• Primary Citation Related Structures: 
  6KNM


• 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, 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.

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Organizational Affiliation: 
• 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.
Therapeutic Discovery, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 60.28 kDa 
• Atom Count: 3,747 
• Modeled Residue Count: 480 
• Deposited Residue Count: 536 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apelin receptor,Rubredoxin,Apelin receptor	A [auth B]	407	Homo sapiens, Clostridium pasteurianum	Mutation(s): 5  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	P35414P00268

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Single domain antibody JN241	B [auth A]	129	Camelus bactrianus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.305 (Depositor), 0.312 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.261 (DCC) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.78	α = 90
b = 48.39	β = 90
c = 350.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Ma, Y.B., Ding, Y., Song, X., Ma, X., Li, X., Zhang, N., Song, Y., Sun, Y., Shen, Y., Zhong, W., Hu, L.A., Ma, Y.L., Zhang, M.Y.

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 1.1: 2020-02-12
  Changes: Advisory, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary