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- EMDB-45992: Structure of PDE6C in complex with the rod inhibitory p gamma sub... -

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Basic information

Entry
Database: EMDB / ID: EMD-45992
TitleStructure of PDE6C in complex with the rod inhibitory p gamma subunit in the absence of added cGMP
Map data
Sample
  • Complex: cone PDE6
    • Protein or peptide: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
  • Protein or peptide: rod pg
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: CYCLIC GUANOSINE MONOPHOSPHATE
KeywordsPDE6-cGMP-GMP complex / HYDROLASE
Function / homology
Function and homology information


retinal cone cell development / 3',5'-cyclic-GMP phosphodiesterase / calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / phototransduction, visible light / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP-mediated signaling / visual perception ...retinal cone cell development / 3',5'-cyclic-GMP phosphodiesterase / calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / phototransduction, visible light / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP-mediated signaling / visual perception / metal ion binding / plasma membrane
Similarity search - Function
3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain ...3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / GAF-like domain superfamily / HD/PDEase domain
Similarity search - Domain/homology
Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSrivastava D / Singh S / Artemyev N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01 EY010843 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural and functional dynamics of human cone cGMP-phosphodiesterase important for photopic vision.
Authors: Sneha Singh / Dhiraj Srivastava / Kimberly Boyd / Nikolai O Artemyev /
Abstract: Cone cGMP-phosphodiesterase (PDE6) is the key effector enzyme for daylight vision, and its properties are critical for shaping distinct physiology of cone photoreceptors. We determined the structures ...Cone cGMP-phosphodiesterase (PDE6) is the key effector enzyme for daylight vision, and its properties are critical for shaping distinct physiology of cone photoreceptors. We determined the structures of human cone PDE6C in various liganded states by single-particle cryo-EM that reveal essential functional dynamics and adaptations of the enzyme. Our analysis exposed the dynamic nature of PDE6C association with its regulatory γ-subunit (Pγ) which allows openings of the catalytic pocket in the absence of phototransduction signaling, thereby controlling photoreceptor noise and sensitivity. We demonstrate evolutionarily recent adaptations of PDE6C stemming from residue substitutions in the Pγ subunit and the noncatalytic cGMP binding site and influencing the Pγ dynamics in holoPDE6C. Thus, our structural analysis sheds light on the previously unrecognized molecular evolution of the effector enzyme in cones that advances adaptation for photopic vision.
History
DepositionJul 31, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45992.png

Downloads & links

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Map

FileDownload / File: emd_45992.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 324 pix.
= 267.948 Å		0.83 Å/pix.
x 324 pix.
= 267.948 Å		0.83 Å/pix.
x 324 pix.
= 267.948 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.85024834 - 1.1796658
Average (Standard dev.)0.0002851752 (±0.037091274)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 267.948 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45992_msk_1.map
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Half map: #2

Fileemd_45992_half_map_1.map
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Half map: #1

Fileemd_45992_half_map_2.map
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Sample components

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Entire : cone PDE6

EntireName: cone PDE6
Components
  • Complex: cone PDE6
    • Protein or peptide: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
  • Protein or peptide: rod pg
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: CYCLIC GUANOSINE MONOPHOSPHATE

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Supramolecule #1: cone PDE6

SupramoleculeName: cone PDE6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 218 KDa

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Macromolecule #1: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'

MacromoleculeName: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: 3',5'-cyclic-GMP phosphodiesterase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.724594 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: GPTSGDYKDD DDKGGEINQV AVEKYLEENP QFAKEYFDRK LRVEVLGEIF KNSQVPVQSS MSFSELTQVE ESALCLELLW TVQEEGGTP EQGVHRALQR LAHLLQADRC SMFLCRSRNG IPEVASRLLD VTPTSKFEDN LVGPDKEVVF PLDIGIVGWA A HTKKTHNV ...String:
GPTSGDYKDD DDKGGEINQV AVEKYLEENP QFAKEYFDRK LRVEVLGEIF KNSQVPVQSS MSFSELTQVE ESALCLELLW TVQEEGGTP EQGVHRALQR LAHLLQADRC SMFLCRSRNG IPEVASRLLD VTPTSKFEDN LVGPDKEVVF PLDIGIVGWA A HTKKTHNV PDVKKNSHFS DFMDKQTGYV TKNLLATPIV VGKEVLAVIM AVNKVNASEF SKQDEEVFSK YLNFVSIILR LH HTSYMYN IESRRSQILM WSANKVFEEL TDVERQFHKA LYTVRSYLNC ERYSIGLLDM TKEKEFYDEW PIKLGEVEPY KGP KTPDGR EVNFYKIIDY ILHGKEEIKV IPTPPADHWT LISGLPTYVA ENGFICNMMN APADEYFTFQ KGPVDETGWV IKNV LSLPI VNKKEDIVGV ATFYNRKDGK PFDEHDEYIT ETLTQFLGWS LLNTDTYDKM NKLENRKDIA QEMLMNQTKA TPEEI KSIL KFQEKLNVDV IDDCEEKQLV AILKEDLPDP RSAELYEFRF SDFPLTEHGL IKCGIRLFFE INVVEKFKVP VEVLTR WMY TVRKGYRAVT YHNWRHGFNV GQTMFTLLMT GRLKKYYTDL EAFAMLAAAF CHDIDHRGTN NLYQMKSTSP LARLHGS SI LERHHLEYSK TLLQDESLNI FQNLNKRQFE TVIHLFEVAI IATDLALYFK KRTMFQKIVD ACEQMQTEEE AIKYVTVD P TKKEIIMAMM MTACDLSAIT KPWEVQSQVA LMVANEFWEQ GDLERTVLQQ QPIPMMDRNK RDELPKLQVG FIDFVCTFV YKEFSRFHKE ITPMLSGLQN NRVEWKSLAD EYDAKMKVIE EEA

UniProtKB: Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'

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Macromolecule #2: rod pg

MacromoleculeName: rod pg / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.055742 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString:
MVGYPYDVPD YAMNLEPPKA EIRSATRVMG GPVTPRKGPP KFKQRQTRQF KSKPPKKGVQ GFGDDIPGME GLGTDITVIC PWEAFNHLE LHELAQYGII

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: CYCLIC GUANOSINE MONOPHOSPHATE

MacromoleculeName: CYCLIC GUANOSINE MONOPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: PCG
Molecular weightTheoretical: 345.205 Da
Chemical component information

ChemComp-PCG:
CYCLIC GUANOSINE MONOPHOSPHATE

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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

Concentration0.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6mzb


Details: homology model of human PDE6C based on PDB 6MZB
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 174400
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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