6JOD

Angiotensin II type 2 receptor with ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Crystal Structure of Angiotensin II Type 2 Receptor with Endogenous Peptide Hormone.

Asada, H.Inoue, A.Ngako Kadji, F.M.Hirata, K.Shiimura, Y.Im, D.Shimamura, T.Nomura, N.Iwanari, H.Hamakubo, T.Kusano-Arai, O.Hisano, H.Uemura, T.Suno, C.Aoki, J.Iwata, S.

(2019) Structure --: --

  • DOI: 10.1016/j.str.2019.12.003

  • PubMed Abstract: 
  • Angiotensin II (AngII) is a peptide hormone that plays a key role in regulating blood pressure, and its interactions with the G protein-coupled receptors, AngII type-1 receptor (AT <sub>1 </sub>R) and AngII type-2 receptor (AT <sub>2 </sub>R), are ce ...

    Angiotensin II (AngII) is a peptide hormone that plays a key role in regulating blood pressure, and its interactions with the G protein-coupled receptors, AngII type-1 receptor (AT 1 R) and AngII type-2 receptor (AT 2 R), are central to its mechanism of action. We solved the crystal structure of human AT 2 R bound to AngII and its specific antibody at 3.2-Å resolution. AngII (full agonist) and [Sar 1 , Ile 8 ]-AngII (partial agonist) interact with AT 2 R in a similar fashion, except at the bottom of the AT 2 R ligand-binding pocket. In particular, the residues including Met128 3.36 , which constitute the deep end of the cavity, play important roles in angiotensin receptor (ATR) activation upon AngII binding. These differences that occur upon endogenous ligand binding may contribute to a structural change in AT 2 R, leading to normalization of the non-canonical coordination of helix 8. Our results will inform the design of more effective ligands for ATRs.


    Organizational Affiliation

    Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan. Electronic address: asada.hidetsugu.4s@kyoto-u.ac.jp.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan; Advanced Research & Development Programs for Medical Innovation (LEAP), Chiyoda, Tokyo 100-0004, Japan.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan.,Molecular Genetics, Institute of Life Science, Kurume University, Fukuoka 830-0011, Japan.,Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan.,RIKEN, SPring-8 Center, Hyogo 679-5165, Japan; Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Saitama 332-0012, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; RIKEN, SPring-8 Center, Hyogo 679-5165, Japan. Electronic address: s.iwata@mfour.med.kyoto-u.ac.jp.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan; Advanced Research & Development Programs for Medical Innovation (PRIME), Chiyoda, Tokyo 100-0004, Japan; Advanced Research & Development Programs for Medical Innovation (LEAP), Chiyoda, Tokyo 100-0004, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type-2 angiotensin II receptor
A
312Homo sapiensMutation(s): 1 
Gene Names: AGTR2
Find proteins for P50052 (Homo sapiens)
Go to Gene View: AGTR2
Go to UniProtKB:  P50052
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Angiotensin II
B
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Soluble cytochrome b562,Soluble cytochrome b562
C
86Escherichia coliMutation(s): 4 
Gene Names: cybC
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of 4A03Fab
H
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Light chain of 4A03Fab
L
212N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.235 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 102.550α = 90.00
b = 426.430β = 90.00
c = 52.700γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXrefinement
MOLREPphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101070

Revision History 

  • Version 1.0: 2020-01-15
    Type: Initial release