8X93: P/Q type calcium channel

P/Q type calcium channel in complex with omega-Agatoxin IVA. Determined by electron microscopy at 2.92 Å resolution. Released 20 Mar 2024.

Method: Electron microscopy
Resolution: 2.92 Å
Organism: Homo sapiens
Chains: 3
Atoms: 21,976
Mol. weight: 478.56 kDa
Ligands: CA, NAG, CLR, PT5
Released: 20 Mar 2024

Explore 8X93 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8X93 contains 126 α-helices and 81 β-strands across 3 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: 75 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	98-116	19
β-strand	121	1	18
β-strand	125	1	18
α-helix	128-134	7
α-helix	137-155	19
α-helix	164-166	3
α-helix	168-184	17
α-helix	193-203	11
α-helix	204-208	5
α-helix	210-222	13
α-helix	226-248	23
α-helix	251-253	3
β-strand	255-258	4	19
β-strand	264	1	19
β-strand	285-288	4	19
α-helix	294-297	4
α-helix	304-315	12
α-helix	320-331	12
α-helix	337-344	8
α-helix	345-350	6
α-helix	351-367	17
α-helix	370-403	34
α-helix	470-484	15
α-helix	486-505	20
α-helix	512-540	29
α-helix	542-547	6
α-helix	549-570	22
α-helix	578-591	14
α-helix	596-608	13
α-helix	610-634	25
α-helix	653-665	13
α-helix	669-679	11
α-helix	687-689	3
α-helix	690-744	55
α-helix	773-788	16
α-helix	1231-1241	11
α-helix	1243-1262	20
α-helix	1271-1297	27
β-strand	1299	1	20
β-strand	1306	1	20
α-helix	1307-1309	3
α-helix	1311-1332	22
α-helix	1338-1345	8
α-helix	1346-1350	5
α-helix	1354-1358	5
α-helix	1360-1375	16
α-helix	1377-1398	22
β-strand	1403-1405	3	21
β-strand	1419-1424	6	22
β-strand	1427-1432	6	22
β-strand	1435-1437	3	21
α-helix	1445-1456	12
α-helix	1461-1470	10
α-helix	1484-1486	3
α-helix	1487-1494	8
α-helix	1495-1501	7
α-helix	1502-1512	11
α-helix	1513-1515	3
α-helix	1530-1538	9
α-helix	1552-1556	5
α-helix	1557-1563	7
α-helix	1565-1583	19
α-helix	1591-1619	29
α-helix	1621-1624	4
α-helix	1628-1648	21
α-helix	1661-1664	4
α-helix	1665-1673	9
α-helix	1675-1689	15
α-helix	1692-1713	22
β-strand	1716	1	23
α-helix	1741-1753	13
α-helix	1757-1763	7
α-helix	1769	1
β-strand	1770	1	23
α-helix	1771	1
α-helix	1786-1811	26
α-helix	1813-1816	4
α-helix	1825-1838	14
β-strand	1845-1847	3	24
α-helix	1848-1857	10
α-helix	1859	1
α-helix	1870-1880	11
β-strand	1883	1	25
α-helix	1884-1885	2
β-strand	1889-1891	3	24
α-helix	1892-1904	13
α-helix	1913-1929	17
α-helix	1935-1941	7
α-helix	1943-1945	3
α-helix	1950	1
β-strand	1951	1	25
α-helix	1952-1981	30

Chain B: 39 helices, 51 β-strands

Element	Residues	Length	Sheet
α-helix	30-51	22
α-helix	55-63	9
β-strand	68-72	5	4
α-helix	75-109	35
β-strand	122-124	3	5
β-strand	125-126	2	6
β-strand	142-144	3	5
β-strand	160	1	7
β-strand	165-167	3	6
α-helix	177-185	9
α-helix	186-188	3
α-helix	189-199	11
β-strand	205-210	6	6
β-strand	215-217	3	6
β-strand	220	1	7
α-helix	222-224	3
α-helix	238-240	3
α-helix	242-248	7
β-strand	253-259	7	8
α-helix	262-264	3
α-helix	267-281	15
β-strand	288-294	7	8
β-strand	298-300	3	8
β-strand	308-309	2	8
α-helix	314-322	9
α-helix	333-343	11
β-strand	356-362	7	8
α-helix	370-376	7
β-strand	383-389	7	8
α-helix	397-405	9
β-strand	410-413	4	8
α-helix	416-418	3
α-helix	419-424	6
α-helix	426-430	5
α-helix	432-435	4
β-strand	445-446	2	6
β-strand	450-451	2	6
β-strand	458-466	9	6
β-strand	486-493	8	6
α-helix	494-499	6
β-strand	511-515	5	9
β-strand	520	1	10
β-strand	521-523	3	9
α-helix	531-533	3
β-strand	556	1	6
β-strand	560	1	10
α-helix	561-564	4
α-helix	569-580	12
β-strand	584-589	6	9
β-strand	592-593	2	11
α-helix	594	1
β-strand	600-601	2	11
β-strand	604-611	8	9
β-strand	618-624	7	9
α-helix	625-628	4
β-strand	629-633	5	4
α-helix	638-645	8
α-helix	650-652	3
β-strand	658-660	3	12
β-strand	667	1	13
α-helix	676-688	13
β-strand	697	1	13
α-helix	699-715	17
α-helix	716-720	5
β-strand	729-736	8	12
β-strand	741-743	3	12
α-helix	746-751	6
α-helix	758-760	3
α-helix	762-768	7
β-strand	773	1	14
β-strand	774-776	3	12
β-strand	792-802	11	12
β-strand	805-816	12	12
α-helix	818-825	8
β-strand	849-854	6	15
β-strand	858	1	16
β-strand	859-862	4	15
α-helix	865-868	4
β-strand	874	1	16
α-helix	875-877	3
α-helix	882-888	7
β-strand	893-899	7	17
β-strand	976-982	7	17
β-strand	990-996	7	15
β-strand	999-1008	10	15
β-strand	1011	1	14
β-strand	1013-1018	6	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
β-strand	115-119	5	1
α-helix	121-131	11
α-helix	156-158	3
β-strand	171-174	4	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	277-280	4
α-helix	287	1
β-strand	288-292	5	3
α-helix	297-305	9
α-helix	310-313	4
α-helix	315-326	12
α-helix	330-332	3
β-strand	335-337	3	3
α-helix	342-359	18

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)
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

>8X93_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 (B), FASTA

>8X93_2 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 3 (A), FASTA

>8X93_3 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
CA	Calcium ion	Ca	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
CLR	Cholesterol	C27 H46 O	5
PT5	[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4…	C47 H85 O19 P3	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	3
3PE	1,2-Distearoyl-sn-glycerophosphoethanolamine	C41 H82 N O8 P	1

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,…
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
8X91 3.11 Å, P/Q type calcium channel in complex with omega-conotoxin MVIIC
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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