7D7M

Cryo-EM Structure of the Prostaglandin E Receptor EP4 Coupled to G Protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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This is version 2.3 of the entry. See complete history


Literature

Cryo-EM Structure of the Prostaglandin E Receptor EP4 Coupled to G Protein.

Nojima, S.Fujita, Y.Kimura, K.T.Nomura, N.Suno, R.Morimoto, K.Yamamoto, M.Noda, T.Iwata, S.Shigematsu, H.Kobayashi, T.

(2021) Structure 29: 252-260.e6

  • DOI: https://doi.org/10.1016/j.str.2020.11.007
  • Primary Citation of Related Structures:  
    7D7M

  • PubMed Abstract: 

    Prostaglandin E receptor EP4, a class A G protein-coupled receptor (GPCR), is a common drug target in various disorders, such as acute decompensated heart failure and ulcerative colitis. Here, we report the cryoelectron microscopy (cryo-EM) structure of the EP4-heterotrimeric G protein (Gs) complex with the endogenous ligand at a global resolution of 3.3 Å. In this structure, compared with that in the inactive EP4 structure, the sixth transmembrane domain is shifted outward on the intracellular side, although the shift is smaller than that in other class A GPCRs bound to Gs. Instead, the C-terminal helix of Gs is inserted toward TM2 of EP4, and the conserved C-terminal hook structure formsthe extended state. These structural features are formed by the conserved residues in prostanoid receptors (Phe54 2.39 and Trp327 7.51 ). These findings may be important for the thorough understanding of the G protein-binding mechanism of EP4 and other prostanoid receptors.


  • Organizational Affiliation

    Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto 606-8501, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prostaglandin E2 receptor EP4 subtype,Prostaglandin E2 receptor EP4 subtype333Homo sapiensMutation(s): 2 
Gene Names: PTGER4PTGER2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P35408 (Homo sapiens)
Explore P35408 
Go to UniProtKB:  P35408
PHAROS:  P35408
GTEx:  ENSG00000171522 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35408
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1345Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
Sequence Annotations
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Entity ID: 3
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 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
Entity Groups  
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UniProt GroupP59768
Sequence Annotations
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short249Homo sapiensMutation(s): 7 
Gene Names: GNASGNAS1GSP
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens)
Explore P63092 
Go to UniProtKB:  P63092
PHAROS:  P63092
GTEx:  ENSG00000087460 
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UniProt GroupP63092
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
nanobody Nb35134Lama glamaMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P2E (Subject of Investigation/LOI)
Query on P2E

Download Ideal Coordinates CCD File 
F [auth A](Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid
C20 H32 O5
XEYBRNLFEZDVAW-ARSRFYASSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
P2E BindingDB:  7D7M Ki: min: 0.11, max: 3.1 (nM) from 3 assay(s)
IC50: min: 0.55, max: 9.9 (nM) from 4 assay(s)
EC50: min: 0.02, max: 7.5 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18-3845
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP19J12880
Japan Agency for Medical Research and Development (AMED)JapanJP20gm0910007
Japan Agency for Medical Research and Development (AMED)JapanJP20am0401020
Japan Agency for Medical Research and Development (AMED)JapanJP20ak0101103
Japan Agency for Medical Research and Development (AMED)JapanJP19am0101115

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 2.0: 2020-12-02
    Type: Coordinate replacement
    Reason: Atoms with unrealistic or zero occupancies
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2020-12-16
    Changes: Database references
  • Version 2.2: 2021-03-17
    Changes: Database references
  • Version 2.3: 2024-10-23
    Changes: Data collection, Database references, Refinement description, Structure summary