9CXH: PDE6C

Structure of PDE6C in complex with the rod inhibitory p gamma subunit in the presence of cGMP. Determined by electron microscopy at 3.1 Å resolution. Released 18 Dec 2024.

Method
Electron microscopy
Resolution
3.1 Å
Organisms
Homo sapiens, Bos taurus
Chains
4
Atoms
13,877
Mol. weight
219.16 kDa
Ligands
5GP, MG, ZN, PCG
Released
18 Dec 2024

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

Secondary structure: helices and β-sheets

9CXH contains 97 α-helices and 38 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: 44 helices, 18 β-strands

ElementResiduesLengthSheet
α-helix23-4119
α-helix55-6915
α-helix76-9116
β-strand94-104111
β-strand107-117111
α-helix123-1264
β-strand12711
β-strand135-13731
α-helix141-1499
β-strand153-15641
α-helix158-1603
α-helix167-1726
β-strand178-18691
β-strand189-19791
α-helix207-25044
α-helix257-26711
β-strand27412
β-strand276-28273
α-helix290-2989
α-helix302-3043
β-strand30814
β-strand31414
β-strand317-32483
β-strand330-33563
α-helix348-3558
β-strand35815
β-strand359-36243
α-helix364-3663
β-strand386-39383
β-strand399-40573
β-strand40812
α-helix413-4142
α-helix416-43116
α-helix434-46027
α-helix462-4632
α-helix464-4707
α-helix473-4764
α-helix487-49711
α-helix499-5002
α-helix518-53114
α-helix535-5384
α-helix542-55514
α-helix564-57916
α-helix589-60012
α-helix611-6177
α-helix620-6245
α-helix629-64315
α-helix655-67117
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: 45 helices, 18 β-strands
ElementResiduesLengthSheet
α-helix37-382
α-helix50-7021
α-helix76-9116
β-strand94-104116
β-strand107-117116
α-helix123-1264
β-strand12716
β-strand135-13736
α-helix142-1498
β-strand153-15536
α-helix158-1603
α-helix167-1726
β-strand179-18686
β-strand189-19796
α-helix207-25044
α-helix257-26711
α-helix269-2724
β-strand27417
β-strand276-28278
α-helix2831
α-helix290-2923
α-helix294-2985
α-helix302-3043
β-strand30819
β-strand31419
β-strand317-32488
β-strand331-33558
α-helix342-3454
α-helix348-3558
β-strand358110
β-strand359-36248
α-helix364-3663
β-strand386-39388
β-strand399-40578
β-strand40817
α-helix413-4142
α-helix416-46045
α-helix462-4632
α-helix464-4685
α-helix474-4774
α-helix487-4959
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-helix655-67117
α-helix674-69219
α-helix697-7059
α-helix708-72417
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: 4 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix26-294
β-strand31110
α-helix32-332
α-helix57-593
α-helix77-837
Chain D: 4 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix27-293
β-strand3115
α-helix32-332
α-helix57-593
α-helix77-837

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'A, Bprotein843Homo sapiensP51160 (AlphaFold model)
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gammaC, Dprotein99Bos taurusP04972 (AlphaFold model)
Sequence of entity 1 (A, B), FASTA
>9CXH_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
>9CXH_2 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma (chains C, D)
MVGYPYDVPDYAMNLEPPKAEIRSATRVMGGPVTPRKGPPKFKQRQTRQFKSKPPKKGVQ
GFGDDIPGMEGLGTDITVICPWEAFNHLELHELAQYGII

Ligands and cofactors

IDNameFormulaCopies
5GPGuanosine-5'-monophosphateC10 H14 N5 O8 P2
MGMagnesium ionMg2
ZNZinc ionZn2
PCGCyclic guanosine monophosphateC10 H12 N5 O7 P2

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:

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