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- EMDB-42238: Bovine rod phosphodiesterase 6 bound to two chimera transducin al... -

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Basic information

Entry
Database: EMDB / ID: EMD-42238
TitleBovine rod phosphodiesterase 6 bound to two chimera transducin alpha subunits without a stabilizing antibody
Map data
Sample
  • Complex: Bovine rod phosphodiesterase 6 bound to two chimera transducin alpha subunits without a stabilizing antibody
Keywordsphosphodiesterase / GPCR effector enzyme / SIGNALING PROTEIN / complex
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.44 Å
AuthorsAplin C / Cerione RA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)1R01EY034867-01 United States
CitationJournal: J Biol Chem / Year: 2024
Title: Probing the mechanism by which the retinal G protein transducin activates its biological effector PDE6.
Authors: Cody Aplin / Richard A Cerione /
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 ...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). Recently, we presented a cryo-EM structure for a complex between two GTP-bound recombinant Gα subunits and native PDE6, that included a bivalent antibody bound to the C-terminal ends of Gα and the inhibitor vardenafil occupying the active sites on the PDEα and PDEβ subunits. We proposed Gα-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 binds to PDE6 in a similar manner as observed when the antibody is present, does Gα 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-PDE6 complexes form with either recombinant or retinal Gα in the absence of the Gα antibody. We show that Gα binding is not necessary for cGMP nor competitive inhibitors to access the active sites; instead, occupancy of the substrate binding sites enables Gα to bind and reposition the PDE6γ subunits to promote catalytic activity. Moreover, we demonstrate by reconstituting Gα-stimulated PDE6 activity in lipid bilayer nanodiscs that the membrane-induced enhancement results from an increase in the apparent binding affinity of Gα for PDE6. These findings provide new insights into how the retinal G protein stimulates rapid catalytic turnover by PDE6 required for dim light vision.
History
DepositionOct 6, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_42238.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.034 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.30970398 - 1.4412881
Average (Standard dev.)-0.0012362611 (±0.04626039)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 310.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42238_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_42238_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Bovine rod phosphodiesterase 6 bound to two chimera transducin al...

EntireName: Bovine rod phosphodiesterase 6 bound to two chimera transducin alpha subunits without a stabilizing antibody
Components
  • Complex: Bovine rod phosphodiesterase 6 bound to two chimera transducin alpha subunits without a stabilizing antibody

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Supramolecule #1: Bovine rod phosphodiesterase 6 bound to two chimera transducin al...

SupramoleculeName: Bovine rod phosphodiesterase 6 bound to two chimera transducin alpha subunits without a stabilizing antibody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Bos taurus (cattle)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 79000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 198342
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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