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- EMDB-9297: Cryo-EM structure of phosphodiesterase 6 -

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Entry
Database: EMDB / ID: 9297
TitleCryo-EM structure of phosphodiesterase 6
Map dataCryo-EM structure of phosphodiesterase 6, primary map
SamplePhosphodiesterase 6
  • (Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit ...) x 2
  • Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
  • ligand
Function / homologyRetinal cGMP phosphodiesterase, gamma subunit / GAF-like domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha / HD/PDEase domain / GAF domain / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / Retinal cGMP phosphodiesterase, gamma subunit superfamily / 3'5'-cyclic nucleotide phosphodiesterase ...Retinal cGMP phosphodiesterase, gamma subunit / GAF-like domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha / HD/PDEase domain / GAF domain / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / Retinal cGMP phosphodiesterase, gamma subunit superfamily / 3'5'-cyclic nucleotide phosphodiesterase / GAF domain / Retinal cGMP phosphodiesterase, gamma subunit / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / Activation of the phototransduction cascade / Inactivation, recovery and regulation of the phototransduction cascade / Ca2+ pathway / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / photoreceptor outer segment membrane / response to stimulus / photoreceptor disc membrane / 3',5'-cyclic-GMP phosphodiesterase / positive regulation of G protein-coupled receptor signaling pathway / cGMP binding / positive regulation of epidermal growth factor receptor signaling pathway / 3',5'-cyclic-GMP phosphodiesterase activity / retina development in camera-type eye / visual perception / regulation of cytosolic calcium ion concentration / activation of MAPK activity / G protein-coupled receptor signaling pathway / zinc ion binding / metal ion binding / Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma / Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha / Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
Function and homology information
SourceBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / 3.4 Å resolution
AuthorsGulati S / Palczewski K / Kovacik L / Stahlberg H
CitationJournal: Sci Adv / Year: 2019
Title: Cryo-EM structure of phosphodiesterase 6 reveals insights into the allosteric regulation of type I phosphodiesterases.
Authors: Sahil Gulati / Krzysztof Palczewski / Andreas Engel / Henning Stahlberg / Lubomir Kovacik
Validation ReportPDB-ID: 6mzb

SummaryFull reportAbout validation report
DateDeposition: Nov 4, 2018 / Header (metadata) release: Mar 6, 2019 / Map release: Mar 6, 2019 / Last update: Mar 13, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6mzb
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9297.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.06 Å/pix.
= 203.136 Å
192 pix
1.06 Å/pix.
= 203.136 Å
192 pix
1.06 Å/pix.
= 203.136 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density
Contour Level:1.0 (by author), 5 (movie #1):
Minimum - Maximum-0.5842323 - 32.156455999999999
Average (Standard dev.)0.15703212 (1.3413881)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin84.084.084.0
Limit275.0275.0275.0
Spacing192192192
CellA=B=C: 203.13599 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0581.0581.058
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z203.136203.136203.136
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS848484
NC/NR/NS192192192
D min/max/mean-0.58432.1560.157

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Supplemental data

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Mask #1

Fileemd_9297_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Phosphodiesterase 6

EntireName: Phosphodiesterase 6 / Number of components: 5

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Component #1: protein, Phosphodiesterase 6

ProteinName: Phosphodiesterase 6 / Recombinant expression: No
SourceSpecies: Bos taurus (cattle)

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Component #2: protein, Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta

ProteinName: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 98.449648 kDa
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Bos taurus (cattle)
Source (natural)Organ or tissue: Eye

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Component #3: protein, Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit...

ProteinName: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 99.461789 kDa
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Bos taurus (cattle)
Source (natural)Organ or tissue: Eye

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Component #4: protein, Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosph...

ProteinName: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.684229 kDa
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Bos taurus (cattle)
Source (natural)Organ or tissue: Eye

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Component #5: ligand, GUANOSINE-3',5'-MONOPHOSPHATE

LigandName: GUANOSINE-3',5'-MONOPHOSPHATE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.345205 kDa

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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: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 8 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 43597
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

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