5XJM

Complex structure of angiotensin II type 2 receptor with Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the human angiotensin II type 2 receptor bound to an angiotensin II analog

Asada, H.Horita, S.Hirata, K.Shiroishi, M.Shiimura, Y.Iwanari, H.Hamakubo, T.Shimamura, T.Nomura, N.Kusano-Arai, O.Uemura, T.Suno, C.Kobayashi, T.Iwata, S.

(2018) Nat. Struct. Mol. Biol. 25: 570-576

  • DOI: 10.1038/s41594-018-0079-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Angiotensin II (AngII) plays a central role in regulating human blood pressure, which is mainly mediated by interactions between AngII and the G-protein-coupled receptors (GPCRs) AngII type 1 receptor (AT <sub>1 </sub>R) and AngII type 2 receptor (AT ...

    Angiotensin II (AngII) plays a central role in regulating human blood pressure, which is mainly mediated by interactions between AngII and the G-protein-coupled receptors (GPCRs) AngII type 1 receptor (AT 1 R) and AngII type 2 receptor (AT 2 R). We have solved the crystal structure of human AT 2 R binding the peptide ligand [Sar 1 , Ile 8 ]AngII and its specific antibody at 3.2-Å resolution. [Sar 1 , Ile 8 ]AngII interacts with both the 'core' binding domain, where the small-molecule ligands of AT 1 R and AT 2 R bind, and the 'extended' binding domain, which is equivalent to the allosteric modulator binding site of muscarinic acetylcholine receptor. We generated an antibody fragment to stabilize the extended binding domain that functions as a positive allosteric modulator. We also identified a signature positively charged cluster, which is conserved among peptide-binding receptors, to locate C termini at the bottom of the binding pocket. The reported results should help with designing ligands for angiotensin receptors and possibly to other peptide GPCRs.


    Organizational Affiliation

    Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,RIKEN, SPring-8 Center, Hyogo, Japan.,Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Saitama, Japan.,Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.,Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Kyoto, Japan.,Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Molecular Genetics, Institute of Life Science, Kurume University, Fukuoka, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan. s.iwata@mfour.med.kyoto-u.ac.jp.,RIKEN, SPring-8 Center, Hyogo, Japan. s.iwata@mfour.med.kyoto-u.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type-2 angiotensin II receptor,Soluble cytochrome b562,Type-2 angiotensin II receptor
A
422Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: cybC, AGTR2
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Angiotensin type II receptor in complex with compound 1 (monoclinic xtals)
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P50052 (Homo sapiens)
Go to Gene View: AGTR2
Go to UniProtKB:  P50052
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FabH
H
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FabL
L
212N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Sar1, Ile8-angiotensin II
B
8Homo sapiensMutation(s): 0 
Gene Names: AGT (SERPINA8)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Angiotensin type II receptor in complex with compound 1 (monoclinic xtals)
Find proteins for P01019 (Homo sapiens)
Go to Gene View: AGT
Go to UniProtKB:  P01019
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SAR
Query on SAR
B
PEPTIDE LINKINGC3 H7 N O2GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 465.390α = 90.00
b = 48.650β = 90.00
c = 55.700γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan15J04343
Japan Society for the Promotion of ScienceJapan15J04343
Japan Society for the Promotion of ScienceJapan22590270
Japan Agency for Medical Research and DevelopmentJapanA19170600003

Revision History 

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-07-18
    Type: Data collection, Database references
  • Version 1.2: 2018-07-25
    Type: Data collection, Database references