8IUK

Cryo-EM structure of the PGF2-alpha-bound human PTGFR-Gq complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 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

Ligand-induced activation and G protein coupling of prostaglandin F 2 alpha receptor.

Wu, C.Xu, Y.He, Q.Li, D.Duan, J.Li, C.You, C.Chen, H.Fan, W.Jiang, Y.Eric Xu, H.

(2023) Nat Commun 14: 2668-2668

  • DOI: https://doi.org/10.1038/s41467-023-38411-x
  • Primary Citation of Related Structures:  
    8IUK, 8IUL, 8IUM

  • PubMed Abstract: 

    Prostaglandin F (PGF ), an endogenous arachidonic acid metabolite, regulates diverse physiological functions in many tissues and cell types through binding and activation of a G-protein-coupled receptor (GPCR), the PGF receptor (FP), which also is the primary therapeutic target for glaucoma and several other diseases. Here, we report cryo-electron microscopy (cryo-EM) structures of the human FP bound to endogenous ligand PGF and anti-glaucoma drugs LTPA and TFPA at global resolutions of 2.67 Å, 2.78 Å, and 3.14 Å. These structures reveal distinct features of FP within the lipid receptor family in terms of ligand binding selectivity, its receptor activation, and G protein coupling mechanisms, including activation in the absence of canonical PIF and ERY motifs and G q coupling through direct interactions with receptor transmembrane helix 1 and intracellular loop 1. Together with mutagenesis and functional studies, our structures reveal mechanisms of ligand recognition, receptor activation, and G protein coupling by FP, which could facilitate rational design of FP-targeting drugs.


  • Organizational Affiliation

    State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. wucanrong@simm.ac.cn.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
G subunit alpha (q)361Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1343Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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Go to UniProtKB:  P62873
PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody fragment scFv16C [auth E]247Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
nanobody Nb35E [auth N]150Lama glamaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Prostaglandin F2-alpha receptorF [auth R]359Homo sapiensMutation(s): 0 
Gene Names: PTGFR
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P43088 (Homo sapiens)
Explore P43088 
Go to UniProtKB:  P43088
PHAROS:  P43088
GTEx:  ENSG00000122420 
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UniProt GroupP43088
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UGU (Subject of Investigation/LOI)
Query on UGU

Download Ideal Coordinates CCD File 
G [auth R](Z)-7-[(1R,2R,3R,5S)-3,5-bis(oxidanyl)-2-[(E,3S)-3-oxidanyloct-1-enyl]cyclopentyl]hept-5-enoic acid
C20 H34 O5
PXGPLTODNUVGFL-YNNPMVKQSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UGU BindingDB:  8IUK Ki: 119 (nM) from 1 assay(s)
IC50: min: 2.5, max: 43 (nM) from 4 assay(s)
EC50: min: 13, max: 79 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81902085

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Structure summary