5XJM

Complex structure of angiotensin II type 2 receptor with Fab

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.230 

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:  
    5XJM, 5XLI

  • 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 1 R) and AngII type 2 receptor (AT 2 R) ...

    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: 

    RIKEN, SPring-8 Center, Hyogo, Japan. s.iwata@mfour.med.kyoto-u.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Type-2 angiotensin II receptor,Soluble cytochrome b562,Type-2 angiotensin II receptorA422Homo sapiens, Escherichia coliMutation(s): 3 
Gene Names: AGTR2, cybC
Membrane Entity: Yes 
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Find proteins for P0ABE7 (Escherichia coli)
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Go to UniProtKB:  P0ABE7
Find proteins for P50052 (Homo sapiens)
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PHAROS:  P50052
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UniProt GroupsP0ABE7P50052
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FabHB [auth H]220Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
FabLC [auth L]212Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Sar1, Ile8-angiotensin IID [auth B]8Homo sapiensMutation(s): 0 
Gene Names: AGT, SERPINA8
Membrane Entity: Yes 
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Find proteins for P01019 (Homo sapiens)
Explore P01019 
Go to UniProtKB:  P01019
PHAROS:  P01019
Entity Groups  
UniProt GroupP01019
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SAR
Query on SAR		D [auth B]PEPTIDE LINKINGC3 H7 N O2GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 465.39α = 90
b = 48.65β = 90
c = 55.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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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  (Full details and data files)

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