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- PDB-6mzb: Cryo-EM structure of phosphodiesterase 6 -

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Basic information

Entry
Database: PDB / ID: 6mzb
TitleCryo-EM structure of phosphodiesterase 6
Components
  • 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
KeywordsSIGNALING PROTEIN / GAF domain / phosphohydrolase / G protein-coupled receptor signaling
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
Specimen sourceBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.4 Å resolution
AuthorsGulati, S. / Palczewski, K.
Funding supportUnited States , 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteEY009339United States
National Institutes of Health/National Human Genome Research InstituteEY027283United States
National Institutes of Health/National Human Genome Research InstituteEY024864United States
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 Report
SummaryFull reportAbout validation report
DateDeposition: Nov 4, 2018 / Release: Mar 6, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 6, 2019Structure modelrepositoryInitial release
1.1Mar 13, 2019Structure modelData collection / Database referencescitation / citation_author / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod

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Assembly

Deposited unit
B: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
A: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha
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)217,9706
Polyers217,2804
Non-polymers6902
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)18280
ΔGint (kcal/M)-107
Surface area (Å2)85370
MethodPISA

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Components

#1: Protein/peptide Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta / GMP-PDE beta


Mass: 98449.648 Da / Num. of mol.: 1 / Source: (gene. exp.) Bos taurus (cattle) / Tissue: Retina / Gene: PDE6B, PDEB / Organ: Eye / Production host: Bos taurus (cattle)
References: UniProt: P23439, 3',5'-cyclic-GMP phosphodiesterase
#2: Protein/peptide Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha / GMP-PDE alpha / PDE V-B1


Mass: 99461.789 Da / Num. of mol.: 1 / Source: (gene. exp.) Bos taurus (cattle) / Tissue: Retina / Gene: PDE6A, PDEA / Organ: Eye / Production host: Bos taurus (cattle)
References: UniProt: P11541, 3',5'-cyclic-GMP phosphodiesterase
#3: Protein/peptide Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma / GMP-PDE gamma


Mass: 9684.229 Da / Num. of mol.: 2 / Source: (gene. exp.) Bos taurus (cattle) / Tissue: Retina / Gene: PDE6G, PDEG / Organ: Eye / Production host: Bos taurus (cattle)
References: UniProt: P04972, 3',5'-cyclic-GMP phosphodiesterase
#4: Chemical ChemComp-35G / GUANOSINE-3',5'-MONOPHOSPHATE


Mass: 345.205 Da / Num. of mol.: 2 / Formula: C10H12N5O7P / Guanosine monophosphate

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Phosphodiesterase 6 / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: NATURAL
Source (natural)Organism: Bos taurus (cattle)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 80 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_3311: / Classification: refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 43597 / Symmetry type: POINT

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