7JSN: PDB entry 7JSN

Structure of the Visual Signaling Complex between Transducin and Phosphodiesterase 6. Determined by electron microscopy at 3.2 Å resolution. Released 21 Oct 2020.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Bos taurus
Chains: 6
Atoms: 19,438
Mol. weight: 304.61 kDa
Ligands: GTP, 35G, VDN, MG
Released: 21 Oct 2020

Explore 7JSN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7JSN contains 119 α-helices and 58 β-strands across 6 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: 42 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	13-15	3
α-helix	22-27	6
α-helix	29-36	8
α-helix	60-65	6
α-helix	76-89	14
β-strand	93-102	10	1
β-strand	105-112	8	1
α-helix	121-123	3
β-strand	125	1	1
α-helix	126-127	2
β-strand	132	1	2
β-strand	133-134	2	1
α-helix	139-147	9
β-strand	151-153	3	1
α-helix	166-169	4
β-strand	177-183	7	1
β-strand	188-195	8	1
α-helix	205-214	10
α-helix	216-248	33
α-helix	255-262	8
β-strand	272-279	8	3
α-helix	288-295	8
α-helix	300-302	3
β-strand	317-322	6	3
β-strand	330-333	4	3
α-helix	347-353	7
β-strand	356	1	4
β-strand	357-359	3	3
α-helix	362-364	3
β-strand	385-391	7	3
β-strand	397-406	10	3
α-helix	414-429	16
α-helix	432-457	26
α-helix	471-474	4
α-helix	479-481	3
α-helix	487-492	6
α-helix	515-528	14
α-helix	532-535	4
α-helix	539-552	14
α-helix	561-576	16
α-helix	581-583	3
α-helix	586-596	11
α-helix	608-613	6
α-helix	618-621	4
α-helix	626-639	14
α-helix	652-666	15
α-helix	671-673	3
α-helix	679-687	9
α-helix	698-702	5
α-helix	706-720	15
α-helix	722-725	4
α-helix	728-751	24
α-helix	756-758	3
α-helix	763-768	6
α-helix	769-779	11
α-helix	783-791	9
α-helix	796-826	31

Chain B: 39 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	47-60	14
α-helix	72-86	15
β-strand	89	1	5
β-strand	92-96	5	6
β-strand	97-100	4	7
β-strand	103-106	4	7
β-strand	110-113	4	6
β-strand	123	1	6
α-helix	124-125	2
β-strand	130	1	8
β-strand	132-133	2	7
α-helix	137-145	9
β-strand	149-151	3	6
α-helix	163-168	6
β-strand	175-182	8	6
β-strand	185-191	7	6
β-strand	195	1	5
α-helix	205-212	8
α-helix	214-246	33
α-helix	253-259	7
β-strand	270	1	9
β-strand	272-278	7	10
α-helix	286-293	8
β-strand	304	1	11
β-strand	310	1	11
β-strand	313-320	8	10
β-strand	328-330	3	10
α-helix	344-350	7
β-strand	353-354	2	12
β-strand	355-357	3	10
α-helix	360-362	3
β-strand	383-389	7	10
β-strand	395-401	7	10
β-strand	404	1	9
α-helix	408-410	3
α-helix	412-427	16
α-helix	429-455	27
α-helix	463-465	3
α-helix	482-492	11
α-helix	494-495	2
α-helix	515-526	12
α-helix	530-533	4
α-helix	537-550	14
α-helix	559-575	17
α-helix	585-594	10
α-helix	606-612	7
α-helix	616-619	4
α-helix	628-636	9
α-helix	650-665	16
α-helix	669-674	6
α-helix	677-688	12
α-helix	692-699	8
α-helix	703-718	16
α-helix	720-722	3
α-helix	729-746	18
α-helix	747-751	5
α-helix	754-756	3
α-helix	757-759	3
α-helix	767-774	8
α-helix	775-779	5
α-helix	780-789	10
α-helix	794-821	28

Chain C: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	2
β-strand	31	1	4
α-helix	42-44	3
α-helix	64-67	4
α-helix	69-73	5

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	8
β-strand	31-32	2	12
α-helix	33	1
α-helix	42-44	3
α-helix	64-67	4
α-helix	69-71	3

Chain E: 16 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	28-36	9	13
α-helix	42-52	11
α-helix	61-64	4
α-helix	67-87	21
α-helix	94-96	3
α-helix	97-109	13
α-helix	111	1
α-helix	117-126	10
α-helix	130-137	8
α-helix	148-151	4
α-helix	155-159	5
β-strand	181-187	7	13
β-strand	190-196	7	13
α-helix	201-210	10
β-strand	216-222	7	13
β-strand	229	1	14
β-strand	237	1	14
α-helix	238-250	13
β-strand	259-265	7	13
α-helix	267-273	7
α-helix	279-281	3
α-helix	292-304	13
β-strand	316-319	4	13
α-helix	326-341	16

Chain F: 15 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	30-36	7	15
α-helix	42-50	9
α-helix	62-86	25
α-helix	89-91	3
α-helix	96-106	11
α-helix	117-127	11
α-helix	132-137	6
α-helix	148-151	4
α-helix	152-154	3
α-helix	155-159	5
α-helix	167-170	4
β-strand	183	1	15
β-strand	192-196	5	15
α-helix	202-208	7
β-strand	216-222	7	15
β-strand	229	1	16
β-strand	237	1	16
α-helix	238-250	13
β-strand	259-265	7	15
α-helix	267-273	7
α-helix	294-304	11
β-strand	316-319	4	15
α-helix	326-341	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha	A	protein	859	Bos taurus	P11541 (AlphaFold model)
Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta	B	protein	853	Bos taurus	P23439 (AlphaFold model)
Guanine nucleotide-binding protein G(t) subunit alpha-1, Guanine nucleotide-binding protein G(i)…	E, F	protein	371	Bos taurus	P04695 (AlphaFold model)
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma	C, D	protein	87	Bos taurus	P04972 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7JSN_1 Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha (chains A)
MGEVTAEEVEKFLDSNVSFAKQYYNLRYRAKVISDLLGPREAAVDFSNYHALNSVEESEI
IFDLLRDFQDNLQAEKCVFNVMKKLCFLLQADRMSLFMYRARNGIAELATRLFNVHKDAV
LEECLVAPDSEIVFPLDMGVVGHVALSKKIVNVPNTEEDEHFCDFVDTLTEYQTKNILAS
PIMNGKDVVAIIMVVNKVDGPHFTENDEEILLKYLNFANLIMKVFHLSYLHNCETRRGQI
LLWSGSKVFEELTDIERQFHKALYTVRAFLNCDRYSVGLLDMTKQKEFFDVWPVLMGEAP
PYAGPRTPDGREINFYKVIDYILHGKEDIKVIPNPPPDHWALVSGLPTYVAQNGLICNIM
NAPSEDFFAFQKEPLDESGWMIKNVLSMPIVNKKEEIVGVATFYNRKDGKPFDEMDETLM
ESLTQFLGWSVLNPDTYELMNKLENRKDIFQDMVKYHVKCDNEEIQTILKTREVYGKEPW
ECEEEELAEILQGELPDADKYEINKFHFSDLPLTELELVKCGIQMYYELKVVDKFHIPQE
ALVRFMYSLSKGYRRITYHNWRHGFNVGQTMFSLLVTGKLKRYFTDLEALAMVTAAFCHD
IDHRGTNNLYQMKSQNPLAKLHGSSILERHHLEFGKTLLRDESLNIFQNLNRRQHEHAIH
MMDIAIIATDLALYFKKRTMFQKIVDQSKTYETQQEWTQYMMLDQTRKEIVMAMMMTACD
LSAITKPWEVQSKVALLVAAEFWEQGDLERTVLQQNPIPMMDRNKADELPKLQVGFIDFV
CTFVYKEFSRFHEEITPMLDGITNNRKEWKALADEYETKMKGLEEEKQKQQAANQAAAGS
QHGGKQPGGGPASKSCCVQ

Sequence of entity 2 (B), FASTA

>7JSN_2 Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta (chains B)
MSLSEGQVHRFLDQNPGFADQYFGRKLSPEDVANACEDGCPEGCTSFRELCQVEESAALF
ELVQDMQENVNMERVVFKILRRLCSILHADRCSLFMYRQRNGVAELATRLFSVQPDSVLE
DCLVPPDSEIVFPLDIGVVGHVAQTKKMVNVQDVMECPHFSSFADELTDYVTRNILATPI
MNGKDVVAVIMAVNKLDGPCFTSEDEDVFLKYLNFGTLNLKIYHLSYLHNCETRRGQVLL
WSANKVFEELTDIERQFHKAFYTVRAYLNCDRYSVGLLDMTKEKEFFDVWPVLMGEAQAY
SGPRTPDGREILFYKVIDYILHGKEDIKVIPSPPADHWALASGLPTYVAESGFICNIMNA
PADEMFNFQEGPLDDSGWIVKNVLSMPIVNKKEEIVGVATFYNRKDGKPFDEQDEVLMES
LTQFLGWSVLNTDTYDKMNKLENRKDIAQDMVLYHVRCDREEIQLILPTRERLGKEPADC
EEDELGKILKEVLPGPAKFDIYEFHFSDLECTELELVKCGIQMYYELGVVRKFQIPQEVL
VRFLFSVSKGYRRITYHNWRHGFNVAQTMFTLLMTGKLKSYYTDLEAFAMVTAGLCHDID
HRGTNNLYQMKSQNPLAKLHGSSILERHHLEFGKFLLSEETLNIYQNLNRRQHEHVIHLM
DIAIIATDLALYFKKRTMFQKIVDESKNYEDRKSWVEYLSLETTRKEIVMAMMMTACDLS
AITKPWEVQSKVALLVAAEFWEQGDLERTVLDQQPIPMMDRNKAAELPKLQVGFIDFVCT
FVYKEFSRFHEEILPMFDRLQNNRKEWKALADEYEAKVKALEEDQKKETTAKKVGTEICN
GGPAPRSSTCRIL

Sequence of entity 3 (E, F), FASTA

>7JSN_3 Guanine nucleotide-binding protein G(t) subunit alpha-1, Guanine nucleotide-binding protein G(i) subunit alpha-1 chimera (chains E, F)
MAHHHHHHAMGAGASAEEKHSRELEKKLKEDAEKDARTVKLLLLGAGESGKSTIVKQMKI
IHQDGYSLEECLEFIAIIYGNTLQSILAIVRAMTTLNIQYGDSARQDDARKLMHMADTIE
EGTMPKEMSDIIQRLWKDSGIQACFDRASEYQLNDSAGYYLSDLERLVTPGYVPTEQDVL
RSCVKTTGIIETQFSFKDLNFRMFDVGGLRSERKKWIHCFEGVTAIIFCVALSDYDMVLV
EDDEVNRMHESMHLFNSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLSICFPDYAGSNT
YEEAGNYIKVQFLELNMRRDVKEIYSHMTCATDTQNVKFVFDAVTDIIIKENLKDCGLFA
AATETSQVAPA

Sequence of entity 4 (C, D), FASTA

>7JSN_4 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma (chains C, D)
MNLEPPKAEIRSATRVMGGPVTPRKGPPKFKQRQTRQFKSKPPKKGVQGFGDDIPGMEGL
GTDITVICPWEAFNHLELHELAQYGII

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
35G	Guanosine-3',5'-monophosphate	C10 H12 N5 O7 P	2
VDN	2-{2-ethoxy-5-[(4-ethylpiperazin-1-yl)sulfonyl]phenyl}-5-methyl-7-propylimidazo…	C23 H32 N6 O4 S	2
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	2

Primary citation

Structure of the Visual Signaling Complex between Transducin and Phosphodiesterase 6. Gao, Y., Eskici, G., Ramachandran, S. et al. Mol Cell (2020) 80:237. DOI 10.1016/j.molcel.2020.09.013 · PubMed

Other PDB entries of the same protein (UniProt P11541 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9OHM 2.72 Å, Cryo-EM structure of bovine phosphodiesterase 6 bound to CB-5083
8UGB 3.0 Å, Cryo-EM structure of bovine phosphodiesterase 6 bound to udenafil
8UFI 3.1 Å, Cryo-EM structure of bovine phosphodiesterase 6
8UGS 3.2 Å, Cryo-EM structure of bovine phosphodiesterase 6 bound to cGMP
8ULG 3.2 Å, Cryo-EM structure of bovine phosphodiesterase 6 bound to IBMX
6MZB 3.4 Å, Cryo-EM structure of phosphodiesterase 6

Browse structure collections

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