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- EMDB-0102: symmetric structure of tPDE6 -

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Basic information

Entry
Database: EMDB / ID: 0102
Titlesymmetric structure of tPDE6
Map data
Sampletruncated, active dimeric complex of PDE6 containing alpha and beta subunits, but no gamma subunitTruncation (disambiguation):
SourceBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / 28 Å resolution
AuthorsQureshi BM / Behrmann E / Loerke J / Spahn CMT / Heck M
CitationJournal: Open Biol / Year: 2018
Title: It takes two transducins to activate the cGMP-phosphodiesterase 6 in retinal rods.
Authors: Bilal M Qureshi / Elmar Behrmann / Johannes Schöneberg / Justus Loerke / Jörg Bürger / Thorsten Mielke / Jan Giesebrecht / Frank Noé / Trevor D Lamb / Klaus Peter Hofmann / Christian M T Spahn / Martin Heck
Abstract: Among cyclic nucleotide phosphodiesterases (PDEs), PDE6 is unique in serving as an effector enzyme in G protein-coupled signal transduction. In retinal rods and cones, PDE6 is membrane-bound and ...Among cyclic nucleotide phosphodiesterases (PDEs), PDE6 is unique in serving as an effector enzyme in G protein-coupled signal transduction. In retinal rods and cones, PDE6 is membrane-bound and activated to hydrolyse its substrate, cGMP, by binding of two active G protein α-subunits (Gα*). To investigate the activation mechanism of mammalian rod PDE6, we have collected functional and structural data, and analysed them by reaction-diffusion simulations. Gα* titration of membrane-bound PDE6 reveals a strong functional asymmetry of the enzyme with respect to the affinity of Gα* for its two binding sites on membrane-bound PDE6 and the enzymatic activity of the intermediary 1 : 1 Gα* · PDE6 complex. Employing cGMP and its 8-bromo analogue as substrates, we find that Gα* · PDE6 forms with high affinity but has virtually no cGMP hydrolytic activity. To fully activate PDE6, it takes a second copy of Gα* which binds with lower affinity, forming Gα* · PDE6 · Gα*. Reaction-diffusion simulations show that the functional asymmetry of membrane-bound PDE6 constitutes a coincidence switch and explains the lack of G protein-related noise in visual signal transduction. The high local concentration of Gα* generated by a light-activated rhodopsin molecule efficiently activates PDE6, whereas the low density of spontaneously activated Gα* fails to activate the effector enzyme.
DateDeposition: Jul 5, 2018 / Header (metadata) release: Aug 22, 2018 / Map release: Sep 5, 2018 / Last update: Sep 5, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

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Map

Fileemd_0102.map.gz (map file in CCP4 format, 1049 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
5.2 Å/pix.
= 332.8 Å
64 pix
5.2 Å/pix.
= 332.8 Å
64 pix
5.2 Å/pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.2 Å
Density
Contour Level:4.0 (by author), 4 (movie #1):
Minimum - Maximum-0.44528803 - 24.389664
Average (Standard dev.)0.37614307 (1.1443177)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin-32.-32.-32.
Limit31.31.31.
Spacing646464
CellA=B=C: 332.8 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.25.25.2
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-0.44524.3900.376

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Supplemental data

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Sample components

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Entire truncated, active dimeric complex of PDE6 containing alpha and be...

EntireName: truncated, active dimeric complex of PDE6 containing alpha and beta subunits, but no gamma subunit
Number of components: 1

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Component #1: protein, truncated, active dimeric complex of PDE6 containing alp...

ProteinName: truncated, active dimeric complex of PDE6 containing alpha and beta subunits, but no gamma subunitTruncation (disambiguation)
Recombinant expression: No
MassExperimental: 200 kDa
SourceSpecies: Bos taurus (cattle)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI SPIRIT
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI EAGLE (2k x 2k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 19716
3D reconstructionResolution: 28 Å / Resolution method: FSC 0.5 CUT-OFF

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