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- EMDB-0102: symmetric structure of tPDE6 -

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Basic information

Entry
Database: EMDB / ID: EMD-0102
Titlesymmetric structure of tPDE6
Map data
Sample
  • Complex: truncated, active dimeric complex of PDE6 containing alpha and beta subunits, but no gamma subunit
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 28.0 Å
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 ...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.
History
DepositionJul 5, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseSep 5, 2018-
UpdateSep 5, 2018-
Current statusSep 5, 2018Processing site: PDBe / Status: Released

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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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0102.png

Downloads & links

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Map

FileDownload / File: emd_0102.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4. / Movie #1: 4
Minimum - Maximum-0.44528803 - 24.389664
Average (Standard dev.)0.37614307 (±1.1443177)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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
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
Components
  • Complex: truncated, active dimeric complex of PDE6 containing alpha and beta subunits, but no gamma subunit

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Supramolecule #1: truncated, active dimeric complex of PDE6 containing alpha and be...

SupramoleculeName: truncated, active dimeric complex of PDE6 containing alpha and beta subunits, but no gamma subunit
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bos taurus (cattle)
Molecular weightExperimental: 200 KDa

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (2k x 2k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 67839 / Details: manual particle selection
Startup modelType of model: OTHER / Details: common lines from negative stain data
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 19716
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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