9CXJ: PDE6C

Structure of PDE6C in complex with the rod inhibitory p gamma subunit with disordered GafA region. 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
10,227
Mol. weight
217.74 kDa
Ligands
MG, ZN
Released
18 Dec 2024

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

Secondary structure: helices and β-sheets

9CXJ contains 74 α-helices and 20 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: 34 helices, 8 β-strands

ElementResiduesLengthSheet
α-helix232-25019
α-helix257-26711
β-strand276-28271
α-helix2831
α-helix290-2989
β-strand30812
β-strand31412
β-strand317-32481
β-strand330-33561
α-helix348-3558
β-strand358-36251
β-strand386-39381
β-strand399-40571
α-helix412-4143
α-helix416-46045
α-helix462-4632
α-helix464-4707
α-helix473-4775
α-helix487-49711
α-helix499-5002
α-helix518-53114
α-helix542-55514
α-helix564-57916
α-helix583-5864
α-helix589-59911
α-helix611-6177
α-helix620-6245
α-helix629-64315
α-helix655-66915
α-helix670-6723
α-helix674-69219
α-helix697-70610
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-helix799-82426
Chain B: 36 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix232-25019
α-helix257-26711
α-helix269-2724
β-strand27413
β-strand276-28274
α-helix2831
α-helix290-2989
α-helix302-3043
β-strand30815
β-strand31415
β-strand317-32484
β-strand330-33564
α-helix342-3454
α-helix348-3558
β-strand358-36254
α-helix364-3663
β-strand386-39384
β-strand399-40574
β-strand40813
α-helix416-46045
α-helix462-4632
α-helix464-4685
α-helix473-4775
α-helix487-4959
α-helix503-5053
α-helix518-53114
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-helix674-69118
α-helix697-70610
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
Chains C and D: 2 helices, 1 β-strand
ElementResiduesLengthSheet
β-strand29-3134
α-helix32-343
α-helix75-839

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
>9CXJ_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
>9CXJ_2 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma (chains C, D)
MVGYPYDVPDYAMNLEPPKAEIRSATRVMGGPVTPRKGPPKFKQRQTRQFKSKPPKKGVQ
GFGDDIPGMEGLGTDITVICPWEAFNHLELHELAQYGII

Ligands and cofactors

IDNameFormulaCopies
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:

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