9CXG: PDE6C

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

Method
Electron microscopy
Resolution
3.0 Å
Organism
Homo sapiens
Chains
4
Atoms
13,340
Mol. weight
223.44 kDa
Ligands
PCG, ZN, MG, 5GP
Released
18 Dec 2024

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

Secondary structure: helices and β-sheets

9CXG contains 98 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-helix56-6914
α-helix76-9116
β-strand93-104121
β-strand107-117111
α-helix123-1264
β-strand12711
β-strand135-13731
α-helix142-1498
β-strand153-15531
α-helix158-1603
α-helix167-1726
β-strand179-18681
β-strand189-199111
α-helix207-25044
α-helix257-26812
α-helix269-2713
β-strand27412
β-strand276-28273
α-helix2831
α-helix290-2989
α-helix302-3043
β-strand30814
β-strand31414
β-strand317-32483
β-strand330-33563
α-helix348-3558
β-strand357-35825
β-strand359-36243
α-helix364-3663
β-strand386-39383
β-strand399-40683
β-strand40812
α-helix413-4142
α-helix416-43116
α-helix433-46028
α-helix462-4632
α-helix464-4707
α-helix474-4774
α-helix487-49711
α-helix499-5002
α-helix518-53114
α-helix535-5384
α-helix542-55514
α-helix564-57916
α-helix583-5864
α-helix589-60113
α-helix611-6166
α-helix620-6245
α-helix629-64315
α-helix655-67016
α-helix674-69219
α-helix697-7059
α-helix708-72316
α-helix725-7284
α-helix731-75424
α-helix759-7613
α-helix766-7716
α-helix772-7798
α-helix780-7845
α-helix785-79410
α-helix796-7983
α-helix799-82426
Chain B: 44 helices, 18 β-strands
ElementResiduesLengthSheet
α-helix54-7017
α-helix76-9116
β-strand94-104116
β-strand107-117116
α-helix123-1264
β-strand12716
α-helix128-1292
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-helix257-27216
β-strand27417
β-strand276-28278
α-helix2831
α-helix290-2989
α-helix302-3043
β-strand30819
β-strand31419
β-strand317-32488
β-strand331-33558
α-helix348-3558
β-strand358110
β-strand359-36248
α-helix364-3663
β-strand386-39388
β-strand399-40688
β-strand40817
α-helix413-4153
α-helix416-46045
α-helix462-4632
α-helix464-4707
α-helix474-4774
α-helix487-49711
α-helix499-5002
α-helix503-5053
α-helix518-53114
α-helix535-5384
α-helix542-55514
α-helix564-57916
α-helix583-5864
α-helix589-60113
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-helix731-75525
α-helix759-7613
α-helix766-7716
α-helix772-7798
α-helix780-7845
α-helix785-79410
α-helix796-7983
α-helix799-82224
Chain C: 6 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix26-294
β-strand31110
α-helix32-332
α-helix35-373
α-helix57-593
α-helix76-783
α-helix80-834
Chain D: 4 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix27-293
β-strand31-3225
α-helix33-342
α-helix36-394
α-helix77-837

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'A, Bprotein843Homo sapiensP51160 (AlphaFold model)
cone P gammaC, Dprotein123Homo sapiensP61249 (AlphaFold model)
Sequence of entity 1 (A, B), FASTA
>9CXG_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
>9CXG_2 cone P gamma (chains C, D)
MVAWSHPQFEKGGGSGGGSGGSAWSHPQFEKENLYFQGAMGSDSPSLSPPAPSQGPTTPR
KGPPKFKQRQTRQFKSKPPKKGVKGFGDDIPGMEGLGTDITVICPWEAFSHLELHELAQF
GII

Ligands and cofactors

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