3JAB: GafA domain of cone phosphodiesterase 6C
Domain organization and conformational plasticity of the G protein effector, PDE6. Determined by electron microscopy at 11.0 Å resolution. Released 10 Jun 2015.
- Method
- Electron microscopy
- Resolution
- 11.0 Å
- Organisms
- Bos taurus, Mus musculus
- Chains
- 12
- Atoms
- 17,620
- Mol. weight
- 259.46 kDa
- Ligands
- IBM
- Released
- 10 Jun 2015
Explore 3JAB in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3JAB contains 112 α-helices and 118 β-strands across 12 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.
Chains A and M: 10 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 56-66 | 11 | |
| α-helix | 75-91 | 17 | |
| β-strand | 93-104 | 12 | 1 |
| β-strand | 107-117 | 11 | 1 |
| α-helix | 123-126 | 4 | |
| β-strand | 127 | 1 | 1 |
| α-helix | 128-129 | 2 | |
| α-helix | 130-132 | 3 | |
| α-helix | 133-134 | 2 | |
| β-strand | 135-136 | 2 | 1 |
| α-helix | 142-149 | 8 | |
| β-strand | 153-155 | 3 | 1 |
| α-helix | 158-160 | 3 | |
| α-helix | 167-172 | 6 | |
| β-strand | 179-186 | 8 | 1 |
| β-strand | 189-199 | 11 | 1 |
| α-helix | 207-223 | 17 | |
Chains B and N: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 391-403 | 13 | |
| α-helix | 404-406 | 3 | |
| α-helix | 410-425 | 16 | |
| β-strand | 427-435 | 9 | 3 |
| β-strand | 439 | 1 | 4 |
| β-strand | 440-441 | 2 | 3 |
| β-strand | 460 | 1 | 4 |
| α-helix | 464-472 | 9 | |
| β-strand | 476-478 | 3 | 3 |
| β-strand | 502-506 | 5 | 3 |
| β-strand | 516-523 | 8 | 3 |
| α-helix | 535-570 | 36 | |
Chains C and O: 23 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 533-543 | 11 | |
| α-helix | 551-554 | 4 | |
| α-helix | 568-581 | 14 | |
| α-helix | 584-587 | 4 | |
| α-helix | 592-604 | 13 | |
| α-helix | 615-630 | 16 | |
| α-helix | 635-637 | 3 | |
| α-helix | 640-652 | 13 | |
| α-helix | 662-667 | 6 | |
| α-helix | 671-675 | 5 | |
| α-helix | 680-693 | 14 | |
| α-helix | 706-722 | 17 | |
| α-helix | 725-740 | 16 | |
| α-helix | 749-764 | 16 | |
| α-helix | 766-769 | 4 | |
| α-helix | 772-795 | 24 | |
| α-helix | 800-802 | 3 | |
| α-helix | 803-805 | 3 | |
| α-helix | 807-812 | 6 | |
| α-helix | 813-820 | 8 | |
| α-helix | 821-826 | 6 | |
| α-helix | 827-835 | 9 | |
| β-strand | 838 | 1 | 7 |
| α-helix | 840-857 | 18 | |
Chains D and P: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 78-83 | 6 | |
Chains H and Q: 10 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 13 |
| α-helix | 7-9 | 3 | |
| β-strand | 10-13 | 4 | 14 |
| β-strand | 18-25 | 8 | 13 |
| α-helix | 29-31 | 3 | |
| β-strand | 32-39 | 8 | 14 |
| β-strand | 45-51 | 7 | 14 |
| β-strand | 57-59 | 3 | 14 |
| α-helix | 61-63 | 3 | |
| β-strand | 64 | 1 | 13 |
| β-strand | 67-72 | 6 | 13 |
| β-strand | 77-82 | 6 | 13 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-96 | 9 | 14 |
| β-strand | 102-103 | 2 | 14 |
| β-strand | 107-112 | 6 | 14 |
| α-helix | 114-116 | 3 | |
| β-strand | 117 | 1 | 15 |
| α-helix | 118-119 | 2 | |
| β-strand | 120-124 | 5 | 16 |
| β-strand | 136-145 | 10 | 16 |
| β-strand | 146 | 1 | 15 |
| β-strand | 151-154 | 4 | 17 |
| α-helix | 155-157 | 3 | |
| β-strand | 159 | 1 | 17 |
| β-strand | 163-165 | 3 | 16 |
| α-helix | 166-168 | 3 | |
| β-strand | 169-171 | 3 | 16 |
| β-strand | 174-183 | 10 | 16 |
| α-helix | 185-187 | 3 | |
| β-strand | 194-199 | 6 | 17 |
| α-helix | 200-202 | 3 | |
| β-strand | 204-209 | 6 | 17 |
Chains L and R: 7 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-5 | 2 | 8 |
| β-strand | 10-13 | 4 | 9 |
| β-strand | 19-25 | 7 | 8 |
| β-strand | 33-38 | 6 | 9 |
| β-strand | 45-49 | 5 | 9 |
| β-strand | 53-54 | 2 | 9 |
| α-helix | 55 | 1 | |
| β-strand | 62-67 | 6 | 8 |
| β-strand | 70-75 | 6 | 8 |
| α-helix | 80-82 | 3 | |
| β-strand | 85-90 | 6 | 9 |
| α-helix | 96 | 1 | |
| β-strand | 97-98 | 2 | 9 |
| β-strand | 102-106 | 5 | 9 |
| β-strand | 111 | 1 | 10 |
| β-strand | 114-118 | 5 | 11 |
| α-helix | 119-121 | 3 | |
| α-helix | 122-125 | 4 | |
| β-strand | 129-139 | 11 | 11 |
| β-strand | 140 | 1 | 10 |
| β-strand | 145-150 | 6 | 12 |
| β-strand | 153-154 | 2 | 12 |
| β-strand | 159-163 | 5 | 11 |
| α-helix | 164-167 | 4 | |
| β-strand | 173-182 | 10 | 11 |
| α-helix | 183-186 | 4 | |
| β-strand | 191-197 | 7 | 12 |
| β-strand | 205-210 | 6 | 12 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| GafA domain of cone phosphodiesterase 6C | A, M | protein | 180 | Bos taurus | A0A0M3KKT0 (AlphaFold model) |
| GafB domain of phosphodiesterase 2A | B, N | protein | 185 | Bos taurus | P14099 (AlphaFold model) |
| phosphodiesterase 5/6 chimera catalytic domain | C, O | protein | 330 | Bos taurus | P16586 (AlphaFold model), Q28156 (AlphaFold model) |
| phosphodiesterase 6 gamma subunit inhibitory peptide | D, P | protein | 18 | Bos taurus | P04972 |
| IgG1-kappa 2E8 light chain | L, R | protein | 214 | Mus musculus | |
| IgG1-kappa 2E8 heavy chain | H, Q | protein | 221 | Mus musculus | |
Sequence of entity 1 (A, M), FASTA
>3JAB_1 GafA domain of cone phosphodiesterase 6C (chains A, M)
MRLEECNILFELLTEIQDEAGSMEKIVHKTLQRLSQLLAADRCSMFICRSRNGIPEVATR
LLNVTPTSKFEDNLVNPDKETVFPLDIGIAGWVAHTKKFFNIPDVKKNNHFSDYLDKKTG
YTTVNMMAIPITQGKEVLAVVMALNKLNASEFSKEDEEVFKKYLNFISLVLRLEHHHHHH
Sequence of entity 2 (B, N), FASTA
>3JAB_2 GafB domain of phosphodiesterase 2A (chains B, N)
QKLKCECQALLQVAKNLFTHLDDVSVLLQEIITEARNLSNAEICSVFLLDQNELVAKVFD
GGVVDDESYEIRIPADQGIAGHVATTGQILNIPDAYAHPLFYRGVDDSTGFRTRNILCFP
IKNENQEVIGVAELVNKINGPWFSKFDEDLATAFSIYCGISIAHSLLYKKVNEAQYRSHL
ANEMM
Sequence of entity 3 (C, O), FASTA
>3JAB_3 phosphodiesterase 5/6 chimera catalytic domain (chains C, O)
GSHMEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQM
KHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAA
LSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYK
TTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITK
PWPIQQRIAELVATEFWEQGDLERTVLQQQPIPMMDRNKRDELPKLQVGFIDFVCTQLYE
ALTHVSEDCFPLLDGCRKNRQKWQALAEQQ
Sequence of entity 4 (D, P), FASTA
>3JAB_4 phosphodiesterase 6 gamma subunit inhibitory peptide (chains D, P)
WEAFNHLELHELAQYGII
Sequence of entity 5 (L, R), FASTA
>3JAB_5 IgG1-kappa 2E8 light chain (chains L, R)
DIVMTQSQKFMSTSVGDRVSITCKASQNVGTAVAWYQQKPGQSPKLMIYSASNRYTGVPD
RFTGSGSGTDFTLTISNMQSEDLADYFCQQYSSYPLTFGAGTKLELKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSATDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC
Sequence of entity 6 (H, Q), FASTA
>3JAB_6 IgG1-kappa 2E8 heavy chain (chains H, Q)
EVQLQQSGAEVVRSGASVKLSCTASGFNIKDYYIHWVKQRPEKGLEWIGWIDPEIGDTEY
VPKFQGKATMTADTSSNTAYLQLSSLTSEDTAVYYCNAGHDYDRGRFPYWGQGTLVTVSA
AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| IBM | 3-isobutyl-1-methylxanthine | C10 H14 N4 O2 | 4 |
Primary citation
Domain Organization and Conformational Plasticity of the G Protein Effector, PDE6. Zhang, Z., He, F., Constantine, R. et al. J Biol Chem (2015) 290:12833-12843. DOI 10.1074/jbc.M115.647636 · PubMed
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