8X91: P/Q type calcium channel

P/Q type calcium channel in complex with omega-conotoxin MVIIC. Determined by electron microscopy at 3.11 Å resolution. Released 20 Mar 2024.

Method: Electron microscopy
Resolution: 3.11 Å
Organisms: Homo sapiens, Conus magus
Chains: 4
Atoms: 22,269
Mol. weight: 482.08 kDa
Ligands: NAG, PT5, CA, 3PE
Released: 20 Mar 2024

Explore 8X91 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8X91 contains 117 α-helices and 84 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: 71 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	98-116	19
α-helix	129-155	27
α-helix	168-184	17
α-helix	193-196	4
α-helix	197-200	4
α-helix	204-208	5
α-helix	210-247	38
β-strand	249	1	19
β-strand	256-258	3	20
β-strand	264	1	20
β-strand	273	1	21
β-strand	280	1	21
β-strand	285-287	3	20
α-helix	294-297	4
β-strand	301	1	19
α-helix	304-315	12
α-helix	320-330	11
α-helix	337-344	8
α-helix	345-350	6
α-helix	351-367	17
α-helix	370-404	35
α-helix	470-483	14
α-helix	486-505	20
α-helix	512-539	28
α-helix	542-547	6
α-helix	549-570	22
α-helix	578-591	14
α-helix	596-608	13
α-helix	610-635	26
β-strand	641	1	22
β-strand	644	1	22
α-helix	653-665	13
α-helix	669-679	11
α-helix	682-685	4
α-helix	687-689	3
α-helix	690-745	56
α-helix	769-771	3
β-strand	772	1	23
α-helix	773-788	16
α-helix	1231-1241	11
α-helix	1243-1261	19
α-helix	1271-1297	27
α-helix	1307-1309	3
α-helix	1311-1332	22
α-helix	1338-1345	8
α-helix	1346-1350	5
α-helix	1352-1354	3
α-helix	1355-1358	4
α-helix	1360-1375	16
α-helix	1377-1397	21
β-strand	1403-1405	3	24
β-strand	1419-1422	4	25
β-strand	1429-1432	4	25
β-strand	1435-1437	3	24
α-helix	1445-1456	12
α-helix	1461-1469	9
α-helix	1484-1486	3
α-helix	1487-1494	8
α-helix	1495-1501	7
α-helix	1502-1511	10
α-helix	1513	1
β-strand	1514	1	23
α-helix	1515	1
α-helix	1528-1538	11
α-helix	1555-1562	8
α-helix	1565-1583	19
α-helix	1591-1619	29
α-helix	1621-1624	4
α-helix	1628-1649	22
α-helix	1658-1660	3
α-helix	1661-1664	4
α-helix	1665-1672	8
α-helix	1675-1690	16
α-helix	1692-1712	21
α-helix	1741-1753	13
α-helix	1757-1763	7
β-strand	1768	1	26
β-strand	1781	1	26
α-helix	1786-1811	26
α-helix	1813-1816	4
α-helix	1825-1838	14
β-strand	1845-1847	3	27
α-helix	1849-1857	9
α-helix	1859	1
α-helix	1870-1880	11
β-strand	1883	1	28
β-strand	1889-1891	3	27
α-helix	1892-1904	13
α-helix	1914-1929	16
α-helix	1935-1941	7
β-strand	1951	1	28
α-helix	1952-1978	27

Chain B: 32 helices, 48 β-strands

Element	Residues	Length	Sheet
α-helix	30-52	23
α-helix	54-63	10
β-strand	68-72	5	5
α-helix	75-110	36
β-strand	122-124	3	6
β-strand	142-144	3	6
β-strand	160	1	7
β-strand	165-167	3	8
α-helix	177-187	11
α-helix	189-199	11
β-strand	205-210	6	8
β-strand	215-217	3	8
β-strand	220	1	7
α-helix	222-224	3
α-helix	242-248	7
β-strand	253-259	7	9
α-helix	267-280	14
β-strand	288-294	7	9
β-strand	298-300	3	9
β-strand	308-309	2	9
α-helix	314-323	10
α-helix	333-343	11
β-strand	356-362	7	9
α-helix	370-376	7
β-strand	383-389	7	9
α-helix	397-405	9
β-strand	410-413	4	9
α-helix	416-418	3
α-helix	419-423	5
α-helix	426-430	5
α-helix	432-436	5
β-strand	445-446	2	8
β-strand	450-451	2	8
β-strand	458-467	10	8
β-strand	484-493	10	8
α-helix	494-499	6
β-strand	511-515	5	10
β-strand	520	1	11
β-strand	521-523	3	10
α-helix	531-533	3
β-strand	560	1	11
α-helix	573-580	8
β-strand	584-589	6	10
β-strand	592-593	2	12
β-strand	600-601	2	12
β-strand	604-611	8	10
β-strand	618-624	7	10
β-strand	629-633	5	5
α-helix	638-645	8
β-strand	658-659	2	13
α-helix	676-689	14
α-helix	699-715	17
α-helix	716-720	5
β-strand	729-736	8	14
β-strand	740-741	2	14
β-strand	742-743	2	13
α-helix	747-751	5
α-helix	758-760	3
α-helix	762-768	7
β-strand	774-776	3	14
β-strand	792-802	11	14
β-strand	805-816	12	14
α-helix	818-825	8
β-strand	849-853	5	15
β-strand	858	1	16
β-strand	859-862	4	15
α-helix	865-868	4
β-strand	874	1	16
α-helix	875-878	4
α-helix	880-888	9
β-strand	893-899	7	17
β-strand	976-982	7	17
β-strand	991-993	3	15
β-strand	996	1	18
β-strand	999	1	18
β-strand	1002-1007	6	15
β-strand	1014-1018	5	15
β-strand	1036-1037	2	17
α-helix	1043-1048	6
α-helix	1050-1052	3

Chain C: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	39-54	16
β-strand	62-66	5	1
β-strand	71	1	2
β-strand	84	1	1
β-strand	86	1	2
β-strand	92-95	4	1
β-strand	103-108	6	1
α-helix	113-114	2
β-strand	115-119	5	1
α-helix	121-129	9
α-helix	156-158	3
β-strand	171-173	3	1
β-strand	180-183	4	3
α-helix	191-207	17
β-strand	212-215	4	3
α-helix	247-262	16
β-strand	266-269	4	3
α-helix	278-280	3
β-strand	288-292	5	3
α-helix	297-305	9
α-helix	309-312	4
α-helix	315-327	13
α-helix	330-332	3
β-strand	335-337	3	3
α-helix	342-359	18

Chain X: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	7	1	4
α-helix	10-12	3
β-strand	25	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Voltage-dependent L-type calcium channel subunit beta-3	C	protein	496	Homo sapiens	P54284 (AlphaFold model)
Omega-conotoxin MVIIC	X	protein	26	Conus magus	P37300 (AlphaFold model)
Voltage-dependent calcium channel subunit alpha-2/delta-1	B	protein	1115	Homo sapiens	P54289 (AlphaFold model)
Voltage-dependent P/Q-type calcium channel subunit alpha-1A	A	protein	2549	Homo sapiens	O00555 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>8X91_1 Voltage-dependent L-type calcium channel subunit beta-3 (chains C)
MYDDSYVPGFEDSEAGSADSYTSRPSLDSDVSLEEDRESARREVESQAQQQLERAKHKPV
AFAVRTNVSYCGVLDEECPVQGSGVNFEAKDFLHIKEKYSNDWWIGRLVKEGGDIAFIPS
PQRLESIRLKQEQKARRSGNPSSLSDIGNRRSPPPSLAKQKQKQAEHVPPYDVVPSMRPV
VLVGPSLKGYEVTDMMQKALFDFLKHRFDGRISITRVTADLSLAKRSVLNNPGKRTIIER
SSARSSIAEVQSEIERIFELAKSLQLVVLDADTINHPAQLAKTSLAPIIVFVKVSSPKVL
QRLIRSRGKSQMKHLTVQMMAYDKLVQCPPESFDVILDENQLEDACEHLAEYLEVYWRAT
HHPAPGPGLLGPPSAIPGLQNQQLLGERGEEHSPLERDSLMPSDEASESSRQAWTGSSQR
SSRHLEEDYADAYQDLYQPHRQHTSGLPSANGHDPQDRLLAQDSEHNHSDRNWQRNRPWP
KDSYLEHHHHHHHHHH

Sequence of entity 2 (X), FASTA

>8X91_2 Omega-conotoxin MVIIC (chains X)
CKGKGAPCRKTMYDCCSGSCGRRGKC

Sequence of entity 3 (B), FASTA

>8X91_3 Voltage-dependent calcium channel subunit alpha-2/delta-1 (chains B)
MAAGCLLALTLTLFQSLLIGPSSEEPFPSAVTIKSWVDKMQEDLVTLAKTASGVNQLVDI
YEKYQDLYTVEPNNARQLVEIAARDIEKLLSNRSKALVRLALEAEKVQAAHQWREDFASN
EVVYYNAKDDLDPEKNDSEPGSQRIKPVFIEDANFGRQISYQHAAVHIPTDIYEGSTIVL
NELNWTSALDEVFKKNREEDPSLLWQVFGSATGLARYYPASPWVDNSRTPNKIDLYDVRR
RPWYIQGAASPKDMLILVDVSGSVSGLTLKLIRTSVSEMLETLSDDDFVNVASFNSNAQD
VSCFQHLVQANVRNKKVLKDAVNNITAKGITDYKKGFSFAFEQLLNYNVSRANCNKIIML
FTDGGEERAQEIFNKYNKDKKVRVFTFSVGQHNYDRGPIQWMACENKGYYYEIPSIGAIR
INTQEYLDVLGRPMVLAGDKAKQVQWTNVYLDALELGLVITGTLPVFNITGQFENKTNLK
NQLILGVMGVDVSLEDIKRLTPRFTLCPNGYYFAIDPNGYVLLHPNLQPKPIGVGIPTIN
LRKRRPNIQNPKSQEPVTLDFLDAELENDIKVEIRNKMIDGESGEKTFRTLVKSQDERYI
DKGNRTYTWTPVNGTDYSLALVLPTYSFYYIKAKLEETITQARYSETLKPDNFEESGYTF
IAPRDYCNDLKISDNNTEFLLNFNEFIDRKTPNNPSCNADLINRVLLDAGFTNELVQNYW
SKQKNIKGVKARFVVTDGGITRVYPKEAGENWQENPETYEDSFYKRSLDNDNYVFTAPYF
NKSGPGAYESGIMVSKAVEIYIQGKLLKPAVVGIKIDVNSWIENFTKTSIRDPCAGPVCD
CKRNSDVMDCVILDDGGFLLMANHDDYTNQIGRFFGEIDPSLMRHLVNISVYAFNKSYDY
QSVCEPGAAPKQGAGHRSAYVPSVADILQIGWWATAAAWSILQQFLLSLTFPRLLEAVEM
EDDDFTASLSKQSCITEQTQYFFDNDSKSFSGVLDCGNCSRIFHGEKLMNTNLIFIMVES
KGTCPCDTRLLIQAEQTSDGPNPCDMVKQPRYRKGPDVCFDNNVLEDYTDCGGVSGLNPS
LWYIIGIQFLLLWLVSGSTHRLLLEHHHHHHHHHH

Sequence of entity 4 (A), FASTA

>8X91_4 Voltage-dependent P/Q-type calcium channel subunit alpha-1A (chains A)
MASWSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYKDDDDKGTMARFGDEMPARYGGGGS
GAAAGVVVGSGGGRGAGGSRQGGQPGAQRMYKQSMAQRARTMALYNPIPVRQNCLTVNRS
LFLFSEDNVVRKYAKKITEWPPFEYMILATIIANCIVLALEQHLPDDDKTPMSERLDDTE
PYFIGIFCFEAGIKIIALGFAFHKGSYLRNGWNVMDFVVVLTGILATVGTEFDLRTLRAV
RVLRPLKLVSGIPSLQVVLKSIMKAMIPLLQIGLLLFFAILIFAIIGLEFYMGKFHTTCF
EEGTDDIQGESPAPCGTEEPARTCPNGTKCQPYWEGPNNGITQFDNILFAVLTVFQCITM
EGWTDLLYNSNDASGNTWNWLYFIPLIIIGSFFMLNLVLGVLSGEFAKERERVENRRAFL
KLRRQQQIERELNGYMEWISKAEEVILAEDETDGEQRHPFDALRRTTIKKSKTDLLNPEE
AEDQLADIASVGSPFARASIKSAKLENSTFFHKKERRMRFYIRRMVKTQAFYWTVLSLVA
LNTLCVAIVHYNQPEWLSDFLYYAEFIFLGLFMSEMFIKMYGLGTRPYFHSSFNCFDCGV
IIGSIFEVIWAVIKPGTSFGISVLRALRLLRIFKVTKYWASLRNLVVSLLNSMKSIISLL
FLLFLFIVVFALLGMQLFGGQFNFDEGTPPTNFDTFPAAIMTVFQILTGEDWNEVMYDGI
KSQGGVQGGMVFSIYFIVLTLFGNYTLLNVFLAIAVDNLANAQELTKDEQEEEEAANQKL
ALQKAKEVAEVSPLSAANMSIAVKEQQKNQKPAKSVWEQRTSEMRKQNLLASREALYNEM
DPDERWKAAYTRHLRPDMKTHLDRPLVVDPQENRNNNTNKSRAAEPTVDQRLGQQRAEDF
LRKQARYHDRARDPSGSAGLDARRPWAGSQEAELSREGPYGRESDHHAREGSLEQPGFWE
GEAERGKAGDPHRRHVHRQGGSRESRSGSPRTGADGEHRRHRAHRRPGEEGPEDKAERRA
RHREGSRPARGGEGEGEGPDGGERRRRHRHGAPATYEGDARREDKERRHRRRKENQGSGV
PVSGPNLSTTRPIQQDLGRQDPPLAEDIDNMKNNKLATAESAAPHGSLGHAGLPQSPAKM
GNSTDPGPMLAIPAMATNPQNAASRRTPNNPGNPSNPGPPKTPENSLIVTNPSGTQTNSA
KTARKPDHTTVDIPPACPPPLNHTVVQVNKNANPDPLPKKEEEKKEEEEDDRGEDGPKPM
PPYSSMFILSTTNPLRRLCHYILNLRYFEMCILMVIAMSSIALAAEDPVQPNAPRNNVLR
YFDYVFTGVFTFEMVIKMIDLGLVLHQGAYFRDLWNILDFIVVSGALVAFAFTGNSKGKD
INTIKSLRVLRVLRPLKTIKRLPKLKAVFDCVVNSLKNVFNILIVYMLFMFIFAVVAVQL
FKGKFFHCTDESKEFEKDCRGKYLLYEKNEVKARDREWKKYEFHYDNVLWALLTLFTVST
GEGWPQVLKHSVDATFENQGPSPGYRMEMSIFYVVYFVVFPFFFVNIFVALIIITFQEQG
DKMMEEYSLEKNERACIDFAISAKPLTRHMPQNKQSFQYRMWQFVVSPPFEYTIMAMIAL
NTIVLMMKFYGASVAYENALRVFNIVFTSLFSLECVLKVMAFGILNYFRDAWNIFDFVTV
LGSITDILVTEFGNNFINLSFLRLFRAARLIKLLRQGYTIRILLWTFVQSFKALPYVCLL
IAMLFFIYAIIGMQVFGNIGIDVEDEDSDEDEFQITEHNNFRTFFQALMLLFRSATGEAW
HNIMLSCLSGKPCDKNSGILTRECGNEFAYFYFVSFIFLCSFLMLNLFVAVIMDNFEYLT
RDSSILGPHHLDEYVRVWAEYDPAAWGRMPYLDMYQMLRHMSPPLGLGKKCPARVAYKRL
LRMDLPVADDNTVHFNSTLMALIRTALDIKIAKGGADKQQMDAELRKEMMAIWPNLSQKT
LDLLVTPHKSTDLTVGKIYAAMMIMEYYRQSKAKKLQAMREEQDRTPLMFQRMEPPSPTQ
EGGPGQNALPSTQLDPGGALMAHESGLKESPSWVTQRAQEMFQKTGTWSPEQGPPTDMPN
SQPNSQSVEMREMGRDGYSDSEHYLPMEGQGRAASMPRLPAENQRRRGRPRGNNLSTISD
TSPMKRSASVLGPKARRLDDYSLERVPPEENQRHHQRRRDRSHRASERSLGRYTDVDTGL
GTDLSMTTQSGDLPSKERDQERGRPKDRKHRQHHHHHHHHHHPPPPDKDRYAQERPDHGR
ARARDQRWSRSPSEGREHMAHRQGSSSVSGSPAPSTSGTSTPRRGRRQLPQTPSTPRPHV
SYSPVIRKAGGSGPPQQQQQQQQQQQQQAVARPGRAATSGPRRYPGPTAEPLAGDRPPTG
GHSSGRSPRMERRVPGPARSESPRACRHGGARWPASGPHVSEGPPGPRHHGYYRGSDYDE
ADGPGSGGGEEAMAGAYDAPPPVRHASSGATGRSPRTPRASGPACASPSRHGRRLPNGYY
PAHGLARPRGPGSRKGLHEPYSESDDDWC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
PT5	[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4…	C47 H85 O19 P3	1
CA	Calcium ion	Ca	3
3PE	1,2-Distearoyl-sn-glycerophosphoethanolamine	C41 H82 N O8 P	2
Y01	Cholesterol hemisuccinate	C31 H50 O4	3
CLR	Cholesterol	C27 H46 O	5

Primary citation

Structural basis for different omega-agatoxin IVA sensitivities of the P-type and Q-type Ca v 2.1 channels. Li, Z., Cong, Y., Wu, T. et al. Cell Res (2024) 34:455-457. DOI 10.1038/s41422-024-00940-5 · PubMed

Other PDB entries of the same protein (UniProt P54284 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8WE6 2.9 Å, Human L-type voltage-gated calcium channel Cav1.2 at 2.9 Angstrom resolution
8WE8 2.9 Å, Human L-type voltage-gated calcium channel Cav1.2 in the presence of calciseptine,…
8X93 2.92 Å, P/Q type calcium channel in complex with omega-Agatoxin IVA
8X90 2.95 Å, P/Q type calcium channel
7MIX 3.0 Å, Human N-type voltage-gated calcium channel Cav2.2 in the presence of ziconotide at 3.0…
7UHG 3.0 Å, Human L-type voltage-gated calcium channel Cav1.3 at 3.0 Angstrom resolution
8WE9 3.0 Å, Human L-type voltage-gated calcium channel Cav1.2 (Class I) in the presence of…
7MIY 3.1 Å, Human N-type voltage-gated calcium channel Cav2.2 at 3.1 Angstrom resolution
7UHF 3.1 Å, Human L-type voltage-gated calcium channel Cav1.3 in the presence of cinnarizine at 3.1…
8E59 3.1 Å, Human L-type voltage-gated calcium channel Cav1.3 in the presence of Amiodarone at 3.1…
8EPL 3.1 Å, Human R-type voltage-gated calcium channel Cav2.3 at 3.1 Angstrom resolution
8WE7 3.2 Å, Human L-type voltage-gated calcium channel Cav1.2 in the presence of calciseptine at 3.2…

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