6LPB

Cryo-EM structure of the human PAC1 receptor coupled to an engineered heterotrimeric G protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cryo-EM structure of the human PAC1 receptor coupled to an engineered heterotrimeric G protein.

Kobayashi, K.Shihoya, W.Nishizawa, T.Kadji, F.M.N.Aoki, J.Inoue, A.Nureki, O.

(2020) Nat.Struct.Mol.Biol. 27: 274-280

  • DOI: 10.1038/s41594-020-0386-8

  • PubMed Abstract: 
  • Pituitary adenylate cyclase-activating polypeptide (PACAP) is a pleiotropic neuropeptide hormone. The PACAP receptor PAC1R, which belongs to the class B G-protein-coupled receptors (GPCRs), is a drug target for mental disorders and dry eye syndrome. ...

    Pituitary adenylate cyclase-activating polypeptide (PACAP) is a pleiotropic neuropeptide hormone. The PACAP receptor PAC1R, which belongs to the class B G-protein-coupled receptors (GPCRs), is a drug target for mental disorders and dry eye syndrome. Here, we present a cryo-EM structure of human PAC1R bound to PACAP and an engineered G s heterotrimer. The structure revealed that transmembrane helix TM1 plays an essential role in PACAP recognition. The extracellular domain (ECD) of PAC1R tilts by ~40° compared with that of the glucagon-like peptide-1 receptor (GLP-1R) and thus does not cover the peptide ligand. A functional analysis demonstrated that the PAC1R ECD functions as an affinity trap and is not required for receptor activation, whereas the GLP-1R ECD plays an indispensable role in receptor activation, illuminating the functional diversity of the ECDs in class B GPCRs. Our structural information will facilitate the design and improvement of better PAC1R agonists for clinical applications.


    Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan. nureki@bs.s.u-tokyo.ac.jp.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan. wtrshh9@gmail.com.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pituitary adenylate cyclase-activating polypeptide
P
38Homo sapiensMutation(s): 0 
Gene Names: ADCYAP1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Class B GPCR: PAC1 receptor coupled to engineered heterotrimeric G protein
Find proteins for P18509 (Homo sapiens)
Go to Gene View: ADCYAP1
Go to UniProtKB:  P18509
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pituitary adenylate cyclase-activating polypeptide type I receptor
R
403Homo sapiensMutation(s): 0 
Gene Names: ADCYAP1R1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Class B GPCR: PAC1 receptor coupled to engineered heterotrimeric G protein
Find proteins for P41586 (Homo sapiens)
Go to Gene View: ADCYAP1R1
Go to UniProtKB:  P41586
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
B
351Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Class B GPCR: PAC1 receptor coupled to engineered heterotrimeric G protein
Find proteins for P54311 (Rattus norvegicus)
Go to UniProtKB:  P54311
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
A
249N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
nanobody Nb35
N
137N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
G
68Bos taurusMutation(s): 0 
Gene Names: GNG2
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Class B GPCR: PAC1 receptor coupled to engineered heterotrimeric G protein
Find proteins for P63212 (Bos taurus)
Go to Gene View: GNG2
Go to UniProtKB:  P63212
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-03-25
    Type: Database references