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- PDB-9ohm: Cryo-EM structure of bovine phosphodiesterase 6 bound to CB-5083 -

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Basic information

Entry
Database: PDB / ID: 9ohm
TitleCryo-EM structure of bovine phosphodiesterase 6 bound to CB-5083
Components
  • (Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit ...) x 2
  • Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
KeywordsSIGNALING PROTEIN / GAF domain / phosphohydrolase / G protein-coupled receptor signaling / CB-5083
Function / homology
Function and homology information


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 / photoreceptor outer segment membrane / entrainment of circadian clock by photoperiod / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP 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 / photoreceptor outer segment membrane / entrainment of circadian clock by photoperiod / 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 / retina development in camera-type eye / 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
Chem-JDP / CYCLIC GUANOSINE MONOPHOSPHATE / 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
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsCrawford, J. / Munuganti, R. / Leung, C. / Singh, K. / Gates, E. / Zhu, X. / Bally, M. / Dos Santos, N. / Sharifiaghdam, M. / Nosrati, Z. ...Crawford, J. / Munuganti, R. / Leung, C. / Singh, K. / Gates, E. / Zhu, X. / Bally, M. / Dos Santos, N. / Sharifiaghdam, M. / Nosrati, Z. / Axerio-Cilies, P. / Berezuk, A. / Cholak, S. / Cameron, D. / Subramaniam, S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canada Excellence Research Chair Award Canada
CitationJournal: To Be Published
Title: Cryo-EM-guided subtractive optimization of a novel VCP/p97 inhibitor
Authors: Crawford, J. / Munuganti, R. / Leung, C. / Singh, K. / Gates, E. / Zhu, X. / Bally, M. / Dos Santos, N. / Sharifiaghdam, M. / Nosrati, Z. / Axerio-Cilies, P. / Berezuk, A. / Cholak, S. / ...Authors: Crawford, J. / Munuganti, R. / Leung, C. / Singh, K. / Gates, E. / Zhu, X. / Bally, M. / Dos Santos, N. / Sharifiaghdam, M. / Nosrati, Z. / Axerio-Cilies, P. / Berezuk, A. / Cholak, S. / Cameron, D. / Subramaniam, S.
History
DepositionMay 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha
B: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
C: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
D: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,97712
Polymers217,2804
Non-polymers1,6978
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit ... , 2 types, 2 molecules AB

#1: Protein Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha / GMP-PDE alpha / PDE V-B1


Mass: 99461.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: PDE6A, PDEA / Production host: Bos taurus (domestic cattle)
References: UniProt: P11541, 3',5'-cyclic-GMP phosphodiesterase
#2: Protein Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta / GMP-PDE beta


Mass: 98449.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: PDE6B, PDEB / Production host: Bos taurus (domestic cattle)
References: UniProt: P23439, 3',5'-cyclic-GMP phosphodiesterase

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Protein , 1 types, 2 molecules CD

#3: Protein Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma / GMP-PDE gamma


Mass: 9684.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: PDE6G, PDEG / Production host: Bos taurus (domestic cattle)
References: UniProt: P04972, 3',5'-cyclic-GMP phosphodiesterase

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Non-polymers , 4 types, 8 molecules

#4: Chemical ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE


Mass: 345.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O7P
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-JDP / 1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide / CB-5083


Mass: 413.472 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23N5O2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: phosphodiesterase 6 complex / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 274770 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 104.4 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003414543
ELECTRON MICROSCOPYf_angle_d0.491919661
ELECTRON MICROSCOPYf_chiral_restr0.04092125
ELECTRON MICROSCOPYf_plane_restr0.0042534
ELECTRON MICROSCOPYf_dihedral_angle_d12.06685497

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