8UGB: Bovine phosphodiesterase 6

Cryo-EM structure of bovine phosphodiesterase 6 bound to udenafil. Determined by electron microscopy at 3.0 Å resolution. Released 17 Jan 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Bos taurus
Chains: 4
Atoms: 13,726
Mol. weight: 219.18 kDa
Ligands: ZUD, MG, ZN, PCG
Released: 17 Jan 2024

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

Secondary structure: helices and β-sheets

8UGB contains 99 α-helices and 42 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: 50 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	17-27	11
α-helix	29-37	9
α-helix	54-65	12
α-helix	74-89	16
β-strand	91-102	12	1
β-strand	105-115	11	1
α-helix	121-124	4
β-strand	125	1	1
α-helix	128-130	3
β-strand	132	1	2
β-strand	133-135	3	1
α-helix	140-147	8
β-strand	151-153	3	1
α-helix	165-169	5
β-strand	177-184	8	1
β-strand	187-197	11	1
α-helix	205-248	44
α-helix	255-265	11
α-helix	267-270	4
β-strand	272	1	3
β-strand	274-280	7	4
α-helix	281	1
α-helix	288-295	8
α-helix	300-302	3
β-strand	306	1	5
β-strand	312	1	5
β-strand	315-322	8	4
β-strand	328-333	6	4
α-helix	346-353	8
β-strand	356	1	6
β-strand	357-360	4	4
α-helix	362-364	3
β-strand	384-391	8	4
β-strand	397-403	7	4
β-strand	406	1	3
α-helix	414-429	16
α-helix	432-458	27
α-helix	462-465	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	531-534	4
α-helix	539-552	14
α-helix	561-576	16
α-helix	580-583	4
α-helix	586-597	12
α-helix	608-614	7
α-helix	617-621	5
α-helix	627-640	14
α-helix	642-644	3
α-helix	646-649	4
α-helix	652-668	17
α-helix	671-687	17
α-helix	688-690	3
α-helix	694-703	10
α-helix	706-720	15
α-helix	722-725	4
α-helix	728-734	7
α-helix	739-753	15
α-helix	756-758	3
α-helix	766-768	3
α-helix	769-776	8
α-helix	777-781	5
α-helix	782-791	10
α-helix	793-795	3
α-helix	796-816	21

Chain B: 48 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	9-14	6
α-helix	16-24	9
α-helix	26-28	3
α-helix	48-66	19
α-helix	72-83	12
β-strand	91-100	10	7
β-strand	103-110	8	7
α-helix	119-122	4
β-strand	123	1	7
α-helix	126-128	3
β-strand	131-133	3	7
α-helix	137-145	9
β-strand	149-151	3	7
α-helix	163-168	6
β-strand	175-182	8	7
β-strand	185-193	9	7
α-helix	203-246	44
α-helix	253-263	11
α-helix	265-268	4
β-strand	270	1	8
β-strand	272-278	7	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	338-341	4
α-helix	344-351	8
β-strand	354	1	11
β-strand	355-358	4	9
α-helix	360-362	3
β-strand	373	1	12
β-strand	378	1	12
β-strand	382-389	8	9
β-strand	395-401	7	9
β-strand	404	1	8
α-helix	408-410	3
α-helix	412-427	16
α-helix	430-456	27
α-helix	462-465	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	529-533	5
α-helix	537-550	14
α-helix	559-574	16
α-helix	578-581	4
α-helix	584-595	12
α-helix	606-612	7
α-helix	615-619	5
α-helix	627-638	12
α-helix	640-642	3
α-helix	650-665	16
α-helix	669-674	6
α-helix	676-687	12
α-helix	692-699	8
α-helix	703-718	16
α-helix	726-749	24
α-helix	754-756	3
α-helix	757-759	3
α-helix	764-766	3
α-helix	767-774	8
α-helix	775-779	5
α-helix	780-789	10
α-helix	794-816	23

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	31	1	11

Chain D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	2
β-strand	31	1	6
α-helix	32-33	2

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

>8UGB_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

>8UGB_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

>8UGB_3 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma (chains C, D)
MNLEPPKAEIRSATRVMGGPVTPRKGPPKFKQRQTRQFKSKPPKKGVQGFGDDIPGMEGL
GTDITVICPWEAFNHLELHELAQYGII

Ligands and cofactors

ID	Name	Formula	Copies
ZUD	Udenafil	C25 H36 N6 O4 S	2
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	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
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
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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