8UFI: Bovine phosphodiesterase 6

Cryo-EM structure of bovine phosphodiesterase 6. Determined by electron microscopy at 3.1 Å resolution. Released 17 Jan 2024.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Bos taurus
Chains: 4
Atoms: 14,157
Mol. weight: 218.15 kDa
Ligands: PCG, ZN, MG
Released: 17 Jan 2024

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

Secondary structure: helices and β-sheets

8UFI contains 96 α-helices and 38 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: 47 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	17-27	11
α-helix	29-36	8
α-helix	50-53	4
α-helix	54-66	13
α-helix	74-88	15
β-strand	91	1	1
β-strand	94-101	8	2
β-strand	106-115	10	2
α-helix	121-124	4
β-strand	125	1	2
β-strand	134-135	2	2
α-helix	139-147	9
β-strand	151-153	3	2
α-helix	165-170	6
β-strand	177-184	8	2
β-strand	187-194	8	2
β-strand	197	1	1
α-helix	205-248	44
α-helix	255-265	11
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	330-333	4	4
α-helix	346-353	8
β-strand	355-356	2	6
β-strand	357-360	4	4
α-helix	362-364	3
β-strand	384-389	6	4
β-strand	399-403	5	4
β-strand	406	1	3
α-helix	410-412	3
α-helix	414-429	16
α-helix	432-458	27
α-helix	460-461	2
α-helix	465-467	3
α-helix	484-494	11
α-helix	498-501	4
α-helix	515-528	14
α-helix	531-535	5
α-helix	539-552	14
α-helix	561-576	16
α-helix	580-583	4
α-helix	586-597	12
α-helix	608-613	6
α-helix	617-621	5
α-helix	626-640	15
α-helix	652-667	16
α-helix	671-676	6
α-helix	679-690	12
α-helix	694-703	10
α-helix	706-720	15
α-helix	722-725	4
α-helix	728-748	21
α-helix	749-753	5
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	796-820	25

Chain B: 42 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	9-14	6
α-helix	16-24	9
α-helix	48-67	20
α-helix	72-87	16
β-strand	89-100	12	7
β-strand	103-113	11	7
β-strand	123	1	7
α-helix	126-128	3
β-strand	132-133	2	7
α-helix	138-145	8
β-strand	149-151	3	7
α-helix	163-167	5
β-strand	175-182	8	7
β-strand	185-195	11	7
α-helix	203-212	10
α-helix	214-246	33
α-helix	253-263	11
α-helix	265-268	4
β-strand	270-278	9	8
α-helix	286-294	9
β-strand	304	1	9
β-strand	310	1	9
β-strand	313-320	8	8
β-strand	328-331	4	8
α-helix	338-341	4
α-helix	344-351	8
β-strand	354	1	10
β-strand	355-358	4	8
α-helix	360-362	3
β-strand	382-389	8	8
β-strand	395-404	10	8
α-helix	412-427	16
α-helix	429-456	28
α-helix	462-465	4
α-helix	482-492	11
α-helix	494-495	2
α-helix	513-526	14
α-helix	529-532	4
α-helix	537-550	14
α-helix	560-574	15
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	650-665	16
α-helix	669-688	20
α-helix	692-701	10
α-helix	704-718	15
α-helix	726-746	21
α-helix	747-751	5
α-helix	754-756	3
α-helix	764-766	3
α-helix	767-774	8
α-helix	775-779	5
α-helix	780-789	10
α-helix	791-793	3
α-helix	794-823	30

Chain C: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	28-29	2
β-strand	31-32	2	6
α-helix	33-34	2
α-helix	57-59	3
α-helix	79-83	5

Chain D: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	31	1	10
α-helix	32-34	3
α-helix	57-59	3
α-helix	78-83	6

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

>8UFI_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

>8UFI_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

>8UFI_3 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma (chains C, D)
MNLEPPKAEIRSATRVMGGPVTPRKGPPKFKQRQTRQFKSKPPKKGVQGFGDDIPGMEGL
GTDITVICPWEAFNHLELHELAQYGII

Ligands and cofactors

ID	Name	Formula	Copies
PCG	Cyclic guanosine monophosphate	C10 H12 N5 O7 P	2
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	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
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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