9CXI: PDE6C

Structure of PDE6C in complex with the rod inhibitory p gamma subunit in the absence of added cGMP. Determined by electron microscopy at 3.0 Å resolution. Released 18 Dec 2024.

Method
Electron microscopy
Resolution
3.0 Å
Organisms
Homo sapiens, Mus musculus
Chains
4
Atoms
13,303
Mol. weight
218.43 kDa
Ligands
PCG, MG, ZN
Released
18 Dec 2024

Explore 9CXI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CXI contains 95 α-helices and 40 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 46 helices, 20 β-strands

ElementResiduesLengthSheet
α-helix55-6915
α-helix76-9116
β-strand94-104111
β-strand107-117111
α-helix123-1264
β-strand12711
β-strand135-13731
α-helix141-1499
β-strand15311
β-strand15612
α-helix158-1603
α-helix167-1726
β-strand17812
β-strand179-18681
β-strand189-19791
α-helix207-25044
α-helix257-26711
α-helix268-2703
β-strand27413
β-strand276-28274
α-helix290-2978
α-helix302-3043
β-strand30815
β-strand31415
β-strand317-32484
β-strand330-33564
α-helix342-3454
α-helix348-3558
β-strand35816
β-strand359-36244
α-helix364-3663
β-strand386-39384
β-strand399-40574
β-strand40813
α-helix412-4143
α-helix416-43116
α-helix433-46028
α-helix462-4632
α-helix464-4707
α-helix473-4775
α-helix487-49711
α-helix499-5002
α-helix518-53114
α-helix534-5374
α-helix542-55514
α-helix564-57916
α-helix583-5864
α-helix589-60012
α-helix611-6177
α-helix620-6245
α-helix629-64315
α-helix655-67016
α-helix674-69219
α-helix697-70610
α-helix708-72316
α-helix725-7284
α-helix731-75121
α-helix752-7565
α-helix759-7613
α-helix762-7643
α-helix766-7716
α-helix772-7798
α-helix780-7845
α-helix785-79410
α-helix796-7983
α-helix799-82224
Chain B: 43 helices, 18 β-strands
ElementResiduesLengthSheet
α-helix52-6716
α-helix68-703
α-helix76-9116
β-strand94-104117
β-strand107-117117
α-helix123-1264
β-strand12717
β-strand135-13737
α-helix141-1499
β-strand153-15537
α-helix158-1603
α-helix167-1726
β-strand179-18687
β-strand189-19797
α-helix207-25044
α-helix257-27216
β-strand27418
β-strand276-28279
α-helix2831
α-helix290-2989
α-helix302-3043
β-strand308110
β-strand314110
β-strand317-32489
β-strand331-33559
α-helix342-3454
α-helix348-3558
β-strand358111
β-strand359-36249
α-helix364-3663
β-strand386-39389
β-strand399-40579
β-strand40818
α-helix416-46045
α-helix462-4632
α-helix464-4685
α-helix473-4775
α-helix487-4948
α-helix499-5002
α-helix503-5053
α-helix518-53114
α-helix542-55514
α-helix564-57916
α-helix583-5864
α-helix589-60012
α-helix611-6166
α-helix620-6245
α-helix629-64315
α-helix655-67016
α-helix674-69320
α-helix697-7059
α-helix708-72316
α-helix725-7284
α-helix731-75626
α-helix759-7613
α-helix766-7716
α-helix772-7798
α-helix780-7845
α-helix785-79410
α-helix796-7983
α-helix799-82224
Chain C: 3 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix27-293
β-strand31111
α-helix35-384
α-helix77-837
Chain D: 3 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix27-293
β-strand3116
α-helix32-332
α-helix77-848

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'A, Bprotein843Homo sapiensP51160 (AlphaFold model)
rod pgC, Dprotein99Mus musculusP04972 (AlphaFold model)
Sequence of entity 1 (A, B), FASTA
>9CXI_1 Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' (chains A, B)
GPTSGDYKDDDDKGGEINQVAVEKYLEENPQFAKEYFDRKLRVEVLGEIFKNSQVPVQSS
MSFSELTQVEESALCLELLWTVQEEGGTPEQGVHRALQRLAHLLQADRCSMFLCRSRNGI
PEVASRLLDVTPTSKFEDNLVGPDKEVVFPLDIGIVGWAAHTKKTHNVPDVKKNSHFSDF
MDKQTGYVTKNLLATPIVVGKEVLAVIMAVNKVNASEFSKQDEEVFSKYLNFVSIILRLH
HTSYMYNIESRRSQILMWSANKVFEELTDVERQFHKALYTVRSYLNCERYSIGLLDMTKE
KEFYDEWPIKLGEVEPYKGPKTPDGREVNFYKIIDYILHGKEEIKVIPTPPADHWTLISG
LPTYVAENGFICNMMNAPADEYFTFQKGPVDETGWVIKNVLSLPIVNKKEDIVGVATFYN
RKDGKPFDEHDEYITETLTQFLGWSLLNTDTYDKMNKLENRKDIAQEMLMNQTKATPEEI
KSILKFQEKLNVDVIDDCEEKQLVAILKEDLPDPRSAELYEFRFSDFPLTEHGLIKCGIR
LFFEINVVEKFKVPVEVLTRWMYTVRKGYRAVTYHNWRHGFNVGQTMFTLLMTGRLKKYY
TDLEAFAMLAAAFCHDIDHRGTNNLYQMKSTSPLARLHGSSILERHHLEYSKTLLQDESL
NIFQNLNKRQFETVIHLFEVAIIATDLALYFKKRTMFQKIVDACEQMQTEEEAIKYVTVD
PTKKEIIMAMMMTACDLSAITKPWEVQSQVALMVANEFWEQGDLERTVLQQQPIPMMDRN
KRDELPKLQVGFIDFVCTFVYKEFSRFHKEITPMLSGLQNNRVEWKSLADEYDAKMKVIE
EEA
Sequence of entity 2 (C, D), FASTA
>9CXI_2 rod pg (chains C, D)
MVGYPYDVPDYAMNLEPPKAEIRSATRVMGGPVTPRKGPPKFKQRQTRQFKSKPPKKGVQ
GFGDDIPGMEGLGTDITVICPWEAFNHLELHELAQYGII

Ligands and cofactors

IDNameFormulaCopies
PCGCyclic guanosine monophosphateC10 H12 N5 O7 P2
MGMagnesium ionMg2
ZNZinc ionZn2

Primary citation

Structural and functional dynamics of human cone cGMP-phosphodiesterase important for photopic vision. Singh, S., Srivastava, D., Boyd, K. et al. Proc Natl Acad Sci U S A (2025) 122:e2419732121-e2419732121. DOI 10.1073/pnas.2419732121 · PubMed

Other PDB entries of the same protein (UniProt P51160 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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