6MZB: Phosphodiesterase 6

Cryo-EM structure of phosphodiesterase 6. Determined by electron microscopy at 3.4 Å resolution. Released 6 Mar 2019.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Bos taurus
Chains: 4
Atoms: 14,066
Mol. weight: 218.15 kDa
Ligands: 35G, MG, ZN
Released: 6 Mar 2019

Explore 6MZB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MZB contains 86 α-helices and 43 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, 18 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	21-34	14
α-helix	40-42	3
α-helix	56-65	10
α-helix	76-88	13
β-strand	92-102	11	9
β-strand	105-115	11	9
α-helix	121-123	3
β-strand	125	1	9
β-strand	133-134	2	9
α-helix	139-147	9
β-strand	151-152	2	9
α-helix	156-158	3
α-helix	165-169	5
β-strand	177-184	8	9
β-strand	187-195	9	9
α-helix	205-214	10
α-helix	216-219	4
α-helix	222-249	28
α-helix	255-265	11
β-strand	272	1	10
β-strand	274-280	7	11
α-helix	288-290	3
α-helix	292-296	5
α-helix	300-302	3
β-strand	306	1	12
β-strand	312	1	12
β-strand	315-322	8	11
β-strand	328-333	6	11
α-helix	346-353	8
β-strand	356	1	13
β-strand	357-359	3	11
β-strand	385-391	7	11
β-strand	397-403	7	11
β-strand	406	1	10
α-helix	411-412	2
α-helix	414-429	16
α-helix	432-457	26
α-helix	462-465	4
α-helix	479-481	3
α-helix	484-492	9
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	608-614	7
α-helix	617-621	5
α-helix	626-639	14
α-helix	652-668	17
α-helix	671-676	6
α-helix	680-688	9
α-helix	697-704	8
α-helix	706-720	15
α-helix	723-725	3
α-helix	728-753	26
α-helix	759-761	3
α-helix	763-768	6
α-helix	769-779	11
α-helix	784-791	8
α-helix	797-826	30

Chain B: 38 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	48-65	18
α-helix	72-87	16
β-strand	92-96	5	1
β-strand	98-100	3	2
β-strand	103-105	3	2
β-strand	106	1	3
β-strand	110-113	4	1
α-helix	119-122	4
β-strand	123	1	1
α-helix	126-128	3
β-strand	130	1	4
β-strand	132	1	3
α-helix	138-145	8
β-strand	149-151	3	1
α-helix	163-166	4
β-strand	175-182	8	1
β-strand	185-192	8	1
α-helix	203-212	10
α-helix	217-246	30
α-helix	253-263	11
β-strand	270	1	5
β-strand	272-278	7	6
α-helix	291-293	3
α-helix	298-300	3
β-strand	304	1	7
β-strand	310	1	7
β-strand	313-320	8	6
β-strand	328-330	3	6
α-helix	345-350	6
β-strand	354	1	8
β-strand	355-356	2	6
β-strand	384-389	6	6
β-strand	395-401	7	6
β-strand	404	1	5
α-helix	409-410	2
α-helix	412-427	16
α-helix	430-456	27
α-helix	458-459	2
α-helix	460-465	6
α-helix	469-472	4
α-helix	482-492	11
α-helix	513-526	14
α-helix	537-550	14
α-helix	559-575	17
α-helix	584-595	12
α-helix	606-612	7
α-helix	615-619	5
α-helix	626-636	11
α-helix	650-666	17
α-helix	669-674	6
α-helix	677-685	9
α-helix	692-699	8
α-helix	703-718	16
α-helix	726-750	25
α-helix	757-759	3
α-helix	761-763	3
α-helix	767-777	11
α-helix	782-789	8
α-helix	791-793	3
α-helix	794-822	29

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	31	1	13
α-helix	32-34	3
α-helix	79-83	5

Chain D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	4
β-strand	31	1	8
α-helix	78-80	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta	B	protein	853	Bos taurus	P23439 (AlphaFold model)
Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha	A	protein	859	Bos taurus	P11541 (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 (B), FASTA

>6MZB_1 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 2 (A), FASTA

>6MZB_2 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 3 (C, D), FASTA

>6MZB_3 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma (chains C, D)
MNLEPPKAEIRSATRVMGGPVTPRKGPPKFKQRQTRQFKSKPPKKGVQGFGDDIPGMEGL
GTDITVICPWEAFNHLELHELAQYGII

Ligands and cofactors

ID	Name	Formula	Copies
35G	Guanosine-3',5'-monophosphate	C10 H12 N5 O7 P	2
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	2

Primary citation

Cryo-EM structure of phosphodiesterase 6 reveals insights into the allosteric regulation of type I phosphodiesterases. Gulati, S., Palczewski, K., Engel, A. et al. Sci Adv (2019) 5:eaav4322-eaav4322. DOI 10.1126/sciadv.aav4322 · PubMed

Other PDB entries of the same protein (UniProt P23439 (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
8ULG 3.2 Å, Cryo-EM structure of bovine phosphodiesterase 6 bound to IBMX

Browse structure collections

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