6M1I

CryoEM structure of human PAC1 receptor in complex with PACAP38


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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 structures of PAC1 receptor reveal ligand binding mechanism.

Wang, J.Song, X.Zhang, D.Chen, X.Li, X.Sun, Y.Li, C.Song, Y.Ding, Y.Ren, R.Harrington, E.H.Hu, L.A.Zhong, W.Xu, C.Huang, X.Wang, H.W.Ma, Y.

(2020) Cell Res 30: 436-445

  • DOI: https://doi.org/10.1038/s41422-020-0280-2
  • Primary Citation of Related Structures:  
    6M1H, 6M1I

  • PubMed Abstract: 

    The pituitary adenylate cyclase-activating polypeptide type I receptor (PAC1R) belongs to the secretin receptor family and is widely distributed in the central neural system and peripheral organs. Abnormal activation of the receptor mediates trigeminovascular activation and sensitization, which is highly related to migraine, making PAC1R a potential therapeutic target. Elucidation of PAC1R activation mechanism would benefit discovery of therapeutic drugs for neuronal disorders. PAC1R activity is governed by pituitary adenylate cyclase-activating polypeptide (PACAP), known as a major vasodilator neuropeptide, and maxadilan, a native peptide from the sand fly, which is also capable of activating the receptor with similar potency. These peptide ligands have divergent sequences yet initiate convergent PAC1R activity. It is of interest to understand the mechanism of PAC1R ligand recognition and receptor activity regulation through structural biology. Here we report two near-atomic resolution cryo-EM structures of PAC1R activated by PACAP38 or maxadilan, providing structural insights into two distinct ligand binding modes. The structures illustrate flexibility of the extracellular domain (ECD) for ligands with distinct conformations, where ECD accommodates ligands in different orientations while extracellular loop 1 (ECL1) protrudes to further anchor the ligand bound in the orthosteric site. By structure-guided molecular modeling and mutagenesis, we tested residues in the ligand-binding pockets and identified clusters of residues that are critical for receptor activity. The structures reported here for the first time elucidate the mechanism of specificity and flexibility of ligand recognition and binding for PAC1R, and provide insights toward the design of therapeutic molecules targeting PAC1R.


  • Organizational Affiliation

    Hybrid Modality Engineering, Therapeutic Discovery, Amgen Research, One Amgen Center Dr., Thousand Oaks, CA, 91320, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pituitary adenylate cyclase-activating polypeptide type I receptor406Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P41586 (Homo sapiens)
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Go to UniProtKB:  P41586
GTEx:  ENSG00000078549 
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UniProt GroupP41586
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pituitary adenylate cyclase-activating polypeptide38Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P18509 (Homo sapiens)
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Go to UniProtKB:  P18509
GTEx:  ENSG00000141433 
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UniProt GroupP18509
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 35134Lama glamaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-271Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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Find proteins for P59768 (Homo sapiens)
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GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1341Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
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GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short394Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P63092 (Homo sapiens)
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GTEx:  ENSG00000087460 
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UniProt GroupP63092
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references