8ULG: Bovine phosphodiesterase 6

Cryo-EM structure of bovine phosphodiesterase 6 bound to IBMX. Determined by electron microscopy at 3.2 Å resolution. Released 17 Jan 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Bos taurus
Chains: 4
Atoms: 14,635
Mol. weight: 218.59 kDa
Ligands: IBM, ZN, MG, PCG
Released: 17 Jan 2024

Explore 8ULG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ULG contains 98 α-helices and 40 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: 45 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	7-15	9
α-helix	17-27	11
α-helix	29-37	9
α-helix	54-62	9
α-helix	74-89	16
β-strand	93-102	10	1
β-strand	105-115	11	1
β-strand	125	1	1
α-helix	128-130	3
β-strand	132	1	2
β-strand	134	1	1
α-helix	140-147	8
β-strand	151-153	3	1
α-helix	165-169	5
β-strand	177-183	7	1
β-strand	188-195	8	1
α-helix	205-248	44
α-helix	255-265	11
β-strand	272-280	9	3
α-helix	288-296	9
α-helix	300-302	3
β-strand	306	1	4
β-strand	312	1	4
β-strand	315-322	8	3
β-strand	328-333	6	3
α-helix	346-353	8
β-strand	356	1	5
β-strand	357-360	4	3
α-helix	362-364	3
β-strand	384-391	8	3
β-strand	397-406	10	3
α-helix	414-429	16
α-helix	432-458	27
α-helix	464-467	4
α-helix	471-474	4
α-helix	484-494	11
α-helix	496-497	2
α-helix	498-501	4
α-helix	515-528	14
α-helix	532-535	4
α-helix	539-552	14
α-helix	561-576	16
α-helix	586-597	12
α-helix	608-613	6
α-helix	617-621	5
α-helix	626-640	15
α-helix	642-644	3
α-helix	652-668	17
α-helix	671-675	5
α-helix	678-687	10
α-helix	688-690	3
α-helix	694-701	8
α-helix	705-720	16
α-helix	722-724	3
α-helix	728-752	25
α-helix	756-758	3
α-helix	769-776	8
α-helix	777-781	5
α-helix	782-791	10
α-helix	793-795	3
α-helix	796-824	29
α-helix	825-829	5

Chain B: 49 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	5-13	9
α-helix	16-22	7
α-helix	29-35	7
α-helix	47-68	22
α-helix	73-87	15
β-strand	91-96	6	6
β-strand	97-100	4	7
β-strand	103-106	4	7
β-strand	110	1	6
α-helix	119-121	3
β-strand	123	1	6
α-helix	126-128	3
β-strand	130	1	8
β-strand	133	1	7
α-helix	138-145	8
β-strand	149-151	3	6
α-helix	154-156	3
α-helix	163-168	6
β-strand	175-181	7	6
β-strand	186-193	8	6
α-helix	203-212	10
α-helix	214-246	33
α-helix	253-263	11
β-strand	270-278	9	9
α-helix	286-293	8
α-helix	298-300	3
β-strand	304	1	10
β-strand	310	1	10
β-strand	313-320	8	9
β-strand	326-330	5	9
α-helix	340-342	3
α-helix	344-351	8
β-strand	354	1	11
β-strand	355-357	3	9
β-strand	383-389	7	9
β-strand	395-404	10	9
α-helix	412-427	16
α-helix	429-456	28
α-helix	460-463	4
α-helix	469-472	4
α-helix	477-479	3
α-helix	482-492	11
α-helix	494-495	2
α-helix	513-527	15
α-helix	529-532	4
α-helix	537-550	14
α-helix	559-574	16
α-helix	579-581	3
α-helix	584-595	12
α-helix	606-611	6
α-helix	615-619	5
α-helix	624-638	15
α-helix	640-642	3
α-helix	650-666	17
α-helix	669-674	6
α-helix	677-689	13
α-helix	692-699	8
α-helix	703-718	16
α-helix	720-722	3
α-helix	732-746	15
α-helix	747-751	5
α-helix	754-756	3
α-helix	767-774	8
α-helix	775-779	5
α-helix	780-789	10
α-helix	791-793	3
α-helix	794-820	27
α-helix	821-825	5

Chain C: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	2
β-strand	31	1	5
α-helix	32-34	3
α-helix	75-83	9

Chain D: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	8
α-helix	27-29	3
β-strand	31	1	11
α-helix	75-83	9

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)
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

>8ULG_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

>8ULG_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 (C, D), FASTA

>8ULG_3 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma (chains C, D)
MNLEPPKAEIRSATRVMGGPVTPRKGPPKFKQRQTRQFKSKPPKKGVQGFGDDIPGMEGL
GTDITVICPWEAFNHLELHELAQYGII

Ligands and cofactors

ID	Name	Formula	Copies
IBM	3-isobutyl-1-methylxanthine	C10 H14 N4 O2	2
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	2
PCG	Cyclic guanosine monophosphate	C10 H12 N5 O7 P	2

Primary citation

Probing the mechanism by which the retinal G protein transducin activates its biological effector PDE6. Aplin, C., Cerione, R.A. J Biol Chem (2023) 300:105608-105608. DOI 10.1016/j.jbc.2023.105608 · 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
7JSN 3.2 Å, Structure of the Visual Signaling Complex between Transducin and Phosphodiesterase 6
8UGS 3.2 Å, Cryo-EM structure of bovine phosphodiesterase 6 bound to cGMP
6MZB 3.4 Å, Cryo-EM structure of phosphodiesterase 6

Browse structure collections

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