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- EMDB-75366: Structure of PDE5 PDE6 chimera -

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Entry
Database: EMDB / ID: EMD-75366
TitleStructure of PDE5 PDE6 chimera
Map data
Sample
  • Complex: PDE5-6 chimera rod p gamma complex
    • Complex: PDE5-PDE6 chimera
      • Protein or peptide: cGMP-specific 3',5'-cyclic phosphodiesterase PDE5-PDE6 chimera
    • Complex: rod p gamma
      • Protein or peptide: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
  • Ligand: 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE
  • Ligand: CYCLIC GUANOSINE MONOPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsPhosphodiesterase / HYDROLASE
Function / homology
Function and homology information


Smooth Muscle Contraction / cGMP effects / RHOBTB1 GTPase cycle / cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / positive regulation of G protein-coupled receptor signaling pathway / Ca2+ pathway / cGMP catabolic process ...Smooth Muscle Contraction / cGMP effects / RHOBTB1 GTPase cycle / cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / positive regulation of G protein-coupled receptor signaling pathway / Ca2+ pathway / cGMP catabolic process / photoreceptor outer segment membrane / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of cAMP/PKA signal transduction / visual perception / photoreceptor disc membrane / molecular adaptor activity / positive regulation of MAPK cascade / signal transduction / zinc ion binding / metal ion binding
Similarity search - Function
Retinal cGMP phosphodiesterase, gamma subunit / Retinal cGMP phosphodiesterase, gamma subunit superfamily / Retinal cGMP phosphodiesterase, gamma subunit / 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. ...Retinal cGMP phosphodiesterase, gamma subunit / Retinal cGMP phosphodiesterase, gamma subunit superfamily / Retinal cGMP phosphodiesterase, gamma subunit / 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. / HD/PDEase domain / GAF-like domain superfamily
Similarity search - Domain/homology
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma / Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' / cGMP-specific 3',5'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsSrivastava D / Singh S / Artemyev NO
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI) United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJan 30, 2026-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75366.png

Downloads & links

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Map

FileDownload / File: emd_75366.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 264.544 Å		0.83 Å/pix.
x 320 pix.
= 264.544 Å		0.83 Å/pix.
x 320 pix.
= 264.544 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8267 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-0.8978025 - 1.428287
Average (Standard dev.)-0.00022387215 (±0.03420668)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75366_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_75366_half_map_1.map
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Half map: #1

Fileemd_75366_half_map_2.map
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Sample components

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Entire : PDE5-6 chimera rod p gamma complex

EntireName: PDE5-6 chimera rod p gamma complex
Components
  • Complex: PDE5-6 chimera rod p gamma complex
    • Complex: PDE5-PDE6 chimera
      • Protein or peptide: cGMP-specific 3',5'-cyclic phosphodiesterase PDE5-PDE6 chimera
    • Complex: rod p gamma
      • Protein or peptide: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
  • Ligand: 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE
  • Ligand: CYCLIC GUANOSINE MONOPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: PDE5-6 chimera rod p gamma complex

SupramoleculeName: PDE5-6 chimera rod p gamma complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 226 KDa

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Supramolecule #2: PDE5-PDE6 chimera

SupramoleculeName: PDE5-PDE6 chimera / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #3: rod p gamma

SupramoleculeName: rod p gamma / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: cGMP-specific 3',5'-cyclic phosphodiesterase PDE5-PDE6 chimera

MacromoleculeName: cGMP-specific 3',5'-cyclic phosphodiesterase PDE5-PDE6 chimera
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: 3',5'-cyclic-GMP phosphodiesterase
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 91.715906 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MGEISQETVE KYLEANPQFA KEYFNRKLQV EVPSGGAQAP ASASFPGRTL AEEAALYLEL LEVLLEEAGS VELAAHRALQ RLAQLLQAD RCSMFLCRAR NGTPEVASKL LDVTPTSKFE DNLVVPDREA VFPLDVGIVG WVAHTKKTFN VPDVKKNSHF S DFMDKQTG ...String:
MGEISQETVE KYLEANPQFA KEYFNRKLQV EVPSGGAQAP ASASFPGRTL AEEAALYLEL LEVLLEEAGS VELAAHRALQ RLAQLLQAD RCSMFLCRAR NGTPEVASKL LDVTPTSKFE DNLVVPDREA VFPLDVGIVG WVAHTKKTFN VPDVKKNSHF S DFMDKQTG YVTRNLLATP IVMGKEVLAV FMAVNKVDAS EFSKQDEEVF SKYLSFVSII LKLHHTNYLY NIESRRSQIL MW SANKVFE ELTDVERQFH KALYTVRTYL NCERYSIGLL DMTKEKEFYD EWPVKLGEVE PYKGPKTPDG REVIFYKIID YIL HGKEEI KVIPTPPMDH WTLISGLPTY VAENGFICNM LNAPADEYFT FQKGPVDETG WVIKNVLSLP IVNKKEDIVG VATF YNRKD GKPFDEYDEH IAETLTQFLG WSLLNTDTYE KMNKLMAKQM VTLEVLSYHA SAAEEETREL QSLAAAVVPS AQTLK ITDF SFSDFELSDL ETALCTIRMF TDLNLVQNFQ MKHEVLCKWI LSVKKNYRKN VAYHNWRHAF NTAQCMFAAL KAGKIQ KRL TDLEILALLI AALSHDLDHR GVNNSYIQRS EHPLAQLYCH SIMEHHHFDQ CLMILNSPGN QILSGLSIEE YKTTLKI IK QAILATDLAL YIKRRGEFFE LIMKNQFNLE DPHQKELFLA MLMTACDLSA ITKPWPIQQR IAELVATEFF DQGDRERK E LNIEPADLMN REKKNKIPSM QVGFIDAICL QLYEALTHVS EDCFPLLDGC RKNRQKWQAL AEQQEKTLIN GESSQTKRN

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

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Macromolecule #2: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiestera...

MacromoleculeName: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: 3',5'-cyclic-GMP phosphodiesterase
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 11.855596 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MNLEPPKAEI RSATRVMGGP VTPRKGPPKF KQRQTRQFKS KPPKKGVQGF GDDIPGMEGL GTDITVICP WEAFNHLELH ELAQYGII

UniProtKB: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma

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Macromolecule #3: 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-...

MacromoleculeName: 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE
type: ligand / ID: 3 / Number of copies: 2 / Formula: VIA
Molecular weightTheoretical: 474.576 Da
Chemical component information

ChemComp-VIA:
5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE / medication*YM

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Macromolecule #4: CYCLIC GUANOSINE MONOPHOSPHATE

MacromoleculeName: CYCLIC GUANOSINE MONOPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: PCG
Molecular weightTheoretical: 345.205 Da
Chemical component information

ChemComp-PCG:
CYCLIC GUANOSINE MONOPHOSPHATE

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 158600
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-10oz:
Structure of PDE5 PDE6 chimera

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