8UGS

Cryo-EM structure of bovine phosphodiesterase 6 bound to cGMP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Probing the mechanism by which the retinal G protein transducin activates its biological effector PDE6.

Aplin, C.Cerione, R.A.

(2023) J Biol Chem 300: 105608-105608

  • DOI: https://doi.org/10.1016/j.jbc.2023.105608
  • Primary Citation of Related Structures:  
    8UFI, 8UGB, 8UGS, 8ULG

  • PubMed Abstract: 

    Phototransduction in retinal rods occurs when the G protein-coupled photoreceptor rhodopsin triggers the activation of phosphodiesterase 6 (PDE6) by GTP-bound alpha subunits of the G protein transducin (Gα T ). Recently, we presented a cryo-EM structure for a complex between two GTP-bound recombinant Gα T subunits and native PDE6, that included a bivalent antibody bound to the C-terminal ends of Gα T and the inhibitor vardenafil occupying the active sites on the PDEα and PDEβ subunits. We proposed Gα T -activated PDE6 by inducing a striking reorientation of the PDEγ subunits away from the catalytic sites. However, questions remained including whether in the absence of the antibody Gα T binds to PDE6 in a similar manner as observed when the antibody is present, does Gα T activate PDE6 by enabling the substrate cGMP to access the catalytic sites, and how does the lipid membrane enhance PDE6 activation? Here, we demonstrate that 2:1 Gα T -PDE6 complexes form with either recombinant or retinal Gα T in the absence of the Gα T antibody. We show that Gα T binding is not necessary for cGMP nor competitive inhibitors to access the active sites; instead, occupancy of the substrate binding sites enables Gα T to bind and reposition the PDE6γ subunits to promote catalytic activity. Moreover, we demonstrate by reconstituting Gα T -stimulated PDE6 activity in lipid bilayer nanodiscs that the membrane-induced enhancement results from an increase in the apparent binding affinity of Gα T for PDE6. These findings provide new insights into how the retinal G protein stimulates rapid catalytic turnover by PDE6 required for dim light vision.


  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha859Bos taurusMutation(s): 0 
EC: 3.1.4.35
UniProt
Find proteins for P11541 (Bos taurus)
Explore P11541 
Go to UniProtKB:  P11541
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11541
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta853Bos taurusMutation(s): 0 
EC: 3.1.4.35
UniProt
Find proteins for P23439 (Bos taurus)
Explore P23439 
Go to UniProtKB:  P23439
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23439
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
C, D
87Bos taurusMutation(s): 0 
EC: 3.1.4.35
UniProt
Find proteins for P04972 (Bos taurus)
Explore P04972 
Go to UniProtKB:  P04972
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04972
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCG (Subject of Investigation/LOI)
Query on PCG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth A],
I [auth B],
L [auth B]
CYCLIC GUANOSINE MONOPHOSPHATE
C10 H12 N5 O7 P
ZOOGRGPOEVQQDX-UUOKFMHZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United States1R01EY034867-01

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Database references