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

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Basic information

Entry
Database: EMDB / ID: EMD-9297
TitleCryo-EM structure of phosphodiesterase 6
Map dataCryo-EM structure of phosphodiesterase 6, primary map
Sample
  • Complex: Phosphodiesterase 6
    • Protein or peptide: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
    • Protein or peptide: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha
    • Protein or peptide: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-3',5'-MONOPHOSPHATE
KeywordsGAF domain / phosphohydrolase / G protein-coupled receptor signaling / SIGNALING PROTEIN
Function / homology
Function and homology information


3',5'-cyclic-GMP phosphodiesterase / Inactivation, recovery and regulation of the phototransduction cascade / positive regulation of G protein-coupled receptor signaling pathway / Activation of the phototransduction cascade / Ca2+ pathway / positive regulation of epidermal growth factor receptor signaling pathway / photoreceptor outer segment membrane / entrainment of circadian clock by photoperiod / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity ...3',5'-cyclic-GMP phosphodiesterase / Inactivation, recovery and regulation of the phototransduction cascade / positive regulation of G protein-coupled receptor signaling pathway / Activation of the phototransduction cascade / Ca2+ pathway / positive regulation of epidermal growth factor receptor signaling 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 / cAMP-mediated signaling / visual perception / photoreceptor disc membrane / retina development in camera-type eye / molecular adaptor activity / 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 / GAF-like domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
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 (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGulati S / Palczewski K / Kovacik L / Stahlberg H
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)EY009339 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)EY027283 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)EY024864 United 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 /
Abstract: Cyclic nucleotide phosphodiesterases (PDEs) work in conjunction with adenylate/guanylate cyclases to regulate the key second messengers of G protein-coupled receptor signaling. Previous attempts to ...Cyclic nucleotide phosphodiesterases (PDEs) work in conjunction with adenylate/guanylate cyclases to regulate the key second messengers of G protein-coupled receptor signaling. Previous attempts to determine the full-length structure of PDE family members at high-resolution have been hindered by structural flexibility, especially in their linker regions and N- and C-terminal ends. Therefore, most structure-activity relationship studies have so far focused on truncated and conserved catalytic domains rather than the regulatory domains that allosterically govern the activity of most PDEs. Here, we used single-particle cryo-electron microscopy to determine the structure of the full-length PDE6αβ2γ complex. The final density map resolved at 3.4 Å reveals several previously unseen structural features, including a coiled N-terminal domain and the interface of PDE6γ subunits with the PDE6αβ heterodimer. Comparison of the PDE6αβ2γ complex with the closed state of PDE2A sheds light on the conformational changes associated with the allosteric activation of type I PDEs.
History
DepositionNov 4, 2018-
Header (metadata) releaseMar 6, 2019-
Map releaseMar 6, 2019-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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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
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  • 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

emd_9297.png

Downloads & links

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Map

FileDownload / File: emd_9297.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of phosphodiesterase 6, primary map
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 5
Minimum - Maximum-0.5842323 - 32.156455999999999
Average (Standard dev.)0.15703212 (±1.3413881)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin848484
Dimensions192192192
Spacing192192192
CellA=B=C: 203.13599 Å
α=β=γ: 90.0 °

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
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

Histogram

Histogram (log scale)

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Sample components

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Entire : Phosphodiesterase 6

EntireName: Phosphodiesterase 6
Components
  • Complex: Phosphodiesterase 6
    • Protein or peptide: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
    • Protein or peptide: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha
    • Protein or peptide: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-3',5'-MONOPHOSPHATE

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Supramolecule #1: Phosphodiesterase 6

SupramoleculeName: Phosphodiesterase 6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Bos taurus (cattle)

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Macromolecule #1: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta

MacromoleculeName: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: 3',5'-cyclic-GMP phosphodiesterase
Source (natural)Organism: Bos taurus (cattle) / Organ: Eye / Tissue: Retina
Molecular weightTheoretical: 98.449648 KDa
Recombinant expressionOrganism: Bos taurus (cattle)
SequenceString: MSLSEGQVHR FLDQNPGFAD QYFGRKLSPE DVANACEDGC PEGCTSFREL CQVEESAALF ELVQDMQENV NMERVVFKIL RRLCSILHA DRCSLFMYRQ RNGVAELATR LFSVQPDSVL EDCLVPPDSE IVFPLDIGVV GHVAQTKKMV NVQDVMECPH F SSFADELT ...String:
MSLSEGQVHR FLDQNPGFAD QYFGRKLSPE DVANACEDGC PEGCTSFREL CQVEESAALF ELVQDMQENV NMERVVFKIL RRLCSILHA DRCSLFMYRQ RNGVAELATR LFSVQPDSVL EDCLVPPDSE IVFPLDIGVV GHVAQTKKMV NVQDVMECPH F SSFADELT DYVTRNILAT PIMNGKDVVA VIMAVNKLDG PCFTSEDEDV FLKYLNFGTL NLKIYHLSYL HNCETRRGQV LL WSANKVF EELTDIERQF HKAFYTVRAY LNCDRYSVGL LDMTKEKEFF DVWPVLMGEA QAYSGPRTPD GREILFYKVI DYI LHGKED IKVIPSPPAD HWALASGLPT YVAESGFICN IMNAPADEMF NFQEGPLDDS GWIVKNVLSM PIVNKKEEIV GVAT FYNRK DGKPFDEQDE VLMESLTQFL GWSVLNTDTY DKMNKLENRK DIAQDMVLYH VRCDREEIQL ILPTRERLGK EPADC EEDE LGKILKEVLP GPAKFDIYEF HFSDLECTEL ELVKCGIQMY YELGVVRKFQ IPQEVLVRFL FSVSKGYRRI TYHNWR HGF NVAQTMFTLL MTGKLKSYYT DLEAFAMVTA GLCHDIDHRG TNNLYQMKSQ NPLAKLHGSS ILERHHLEFG KFLLSEE TL NIYQNLNRRQ HEHVIHLMDI AIIATDLALY FKKRTMFQKI VDESKNYEDR KSWVEYLSLE TTRKEIVMAM MMTACDLS A ITKPWEVQSK VALLVAAEFW EQGDLERTVL DQQPIPMMDR NKAAELPKLQ VGFIDFVCTF VYKEFSRFHE EILPMFDRL QNNRKEWKAL ADEYEAKVKA LEEDQKKETT AKKVGTEICN GGPAPRSSTC RIL

UniProtKB: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta

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Macromolecule #2: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha

MacromoleculeName: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: 3',5'-cyclic-GMP phosphodiesterase
Source (natural)Organism: Bos taurus (cattle) / Organ: Eye / Tissue: Retina
Molecular weightTheoretical: 99.461789 KDa
Recombinant expressionOrganism: Bos taurus (cattle)
SequenceString: MGEVTAEEVE KFLDSNVSFA KQYYNLRYRA KVISDLLGPR EAAVDFSNYH ALNSVEESEI IFDLLRDFQD NLQAEKCVFN VMKKLCFLL QADRMSLFMY RARNGIAELA TRLFNVHKDA VLEECLVAPD SEIVFPLDMG VVGHVALSKK IVNVPNTEED E HFCDFVDT ...String:
MGEVTAEEVE KFLDSNVSFA KQYYNLRYRA KVISDLLGPR EAAVDFSNYH ALNSVEESEI IFDLLRDFQD NLQAEKCVFN VMKKLCFLL QADRMSLFMY RARNGIAELA TRLFNVHKDA VLEECLVAPD SEIVFPLDMG VVGHVALSKK IVNVPNTEED E HFCDFVDT LTEYQTKNIL ASPIMNGKDV VAIIMVVNKV DGPHFTENDE EILLKYLNFA NLIMKVFHLS YLHNCETRRG QI LLWSGSK VFEELTDIER QFHKALYTVR AFLNCDRYSV GLLDMTKQKE FFDVWPVLMG EAPPYAGPRT PDGREINFYK VID YILHGK EDIKVIPNPP PDHWALVSGL PTYVAQNGLI CNIMNAPSED FFAFQKEPLD ESGWMIKNVL SMPIVNKKEE IVGV ATFYN RKDGKPFDEM DETLMESLTQ FLGWSVLNPD TYELMNKLEN RKDIFQDMVK YHVKCDNEEI QTILKTREVY GKEPW ECEE EELAEILQGE LPDADKYEIN KFHFSDLPLT ELELVKCGIQ MYYELKVVDK FHIPQEALVR FMYSLSKGYR RITYHN WRH GFNVGQTMFS LLVTGKLKRY FTDLEALAMV TAAFCHDIDH RGTNNLYQMK SQNPLAKLHG SSILERHHLE FGKTLLR DE SLNIFQNLNR RQHEHAIHMM DIAIIATDLA LYFKKRTMFQ KIVDQSKTYE TQQEWTQYMM LDQTRKEIVM AMMMTACD L SAITKPWEVQ SKVALLVAAE FWEQGDLERT VLQQNPIPMM DRNKADELPK LQVGFIDFVC TFVYKEFSRF HEEITPMLD GITNNRKEWK ALADEYETKM KGLEEEKQKQ QAANQAAAGS QHGGKQPGGG PASKSCCVQ

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

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Macromolecule #3: 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: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: 3',5'-cyclic-GMP phosphodiesterase
Source (natural)Organism: Bos taurus (cattle) / Organ: Eye / Tissue: Retina
Molecular weightTheoretical: 9.684229 KDa
Recombinant expressionOrganism: Bos taurus (cattle)
SequenceString:
MNLEPPKAEI RSATRVMGGP VTPRKGPPKF KQRQTRQFKS KPPKKGVQGF GDDIPGMEGL GTDITVICPW EAFNHLELHE LAQYGII

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

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: GUANOSINE-3',5'-MONOPHOSPHATE

MacromoleculeName: GUANOSINE-3',5'-MONOPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: 35G
Molecular weightTheoretical: 345.205 Da
Chemical component information

ChemComp-35G:
GUANOSINE-3',5'-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

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43597
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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