+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0102 | |||||||||
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Title | symmetric structure of tPDE6 | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 28.0 Å | |||||||||
Authors | Qureshi BM / Behrmann E / Loerke J / Spahn CMT / Heck M | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0102.map.gz | 648.2 KB | EMDB map data format | |
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Header (meta data) | emd-0102-v30.xml emd-0102.xml | 8 KB 8 KB | Display Display | EMDB header |
Images | emd_0102.png | 27.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0102 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0102 | HTTPS FTP |
-Validation report
Summary document | emd_0102_validation.pdf.gz | 197.2 KB | Display | EMDB validaton report |
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Full document | emd_0102_full_validation.pdf.gz | 196.4 KB | Display | |
Data in XML | emd_0102_validation.xml.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0102 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0102 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0102.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 5.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : truncated, active dimeric complex of PDE6 containing alpha and be...
Entire | Name: truncated, active dimeric complex of PDE6 containing alpha and beta subunits, but no gamma subunit |
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Components |
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-Supramolecule #1: truncated, active dimeric complex of PDE6 containing alpha and be...
Supramolecule | Name: truncated, active dimeric complex of PDE6 containing alpha and beta subunits, but no gamma subunit type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Experimental: 200 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: FEI EAGLE (2k x 2k) / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |