7JPV: PDB entry 7JPV

Rabbit Cav1.1 in the presence of 1 micromolar (S)-(-)-Bay K8644 in nanodiscs at 3.4 Angstrom resolution. Determined by electron microscopy at 3.4 Å resolution. Released 18 Nov 2020.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Oryctolagus cuniculus
Chains: 3
Atoms: 18,288
Mol. weight: 369.97 kDa
Ligands: PC1, 3PE, CA
Released: 18 Nov 2020

Explore 7JPV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7JPV contains 110 α-helices and 75 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: 62 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	57-64	8
α-helix	81-105	25
α-helix	122-142	21
α-helix	162-165	4
α-helix	166-170	5
α-helix	173-178	6
α-helix	180-192	13
α-helix	197-217	21
β-strand	225-228	4	1
β-strand	234	1	1
α-helix	252-254	3
β-strand	259-262	4	1
α-helix	278-289	12
α-helix	294-301	8
α-helix	311-345	35
α-helix	434-449	16
α-helix	458-486	29
α-helix	488-490	3
α-helix	495-497	3
α-helix	500-514	15
α-helix	521-529	9
α-helix	530-536	7
α-helix	537-541	5
α-helix	543-581	39
α-helix	600-611	12
α-helix	616-626	11
α-helix	632-635	4
α-helix	636-639	4
α-helix	640-646	7
α-helix	648-656	9
α-helix	664-672	9
α-helix	799-810	12
α-helix	814-817	4
α-helix	829-851	23
α-helix	869-880	12
α-helix	894-898	5
α-helix	908-911	4
α-helix	914-927	14
α-helix	930-949	20
β-strand	955-956	2	2
β-strand	971-975	5	3
α-helix	976-978	3
β-strand	983-987	5	3
β-strand	991-992	2	2
α-helix	993	1
α-helix	1000-1011	12
α-helix	1016-1023	8
α-helix	1032-1034	3
α-helix	1044-1047	4
α-helix	1051-1056	6
α-helix	1057-1071	15
α-helix	1085-1094	10
α-helix	1106-1115	10
α-helix	1118-1136	19
α-helix	1153-1170	18
α-helix	1181-1205	25
α-helix	1233-1236	4
α-helix	1237-1240	4
α-helix	1241-1248	8
α-helix	1251-1261	11
α-helix	1270-1288	19
β-strand	1292	1	4
β-strand	1301	1	5
β-strand	1304	1	5
α-helix	1309-1321	13
α-helix	1325-1331	7
β-strand	1336	1	6
α-helix	1337	1
β-strand	1338	1	4
α-helix	1339	1
β-strand	1352	1	6
α-helix	1357-1380	24
α-helix	1384-1387	4
α-helix	1396-1409	14
α-helix	1426-1428	3

Chain E: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	7-28	22
α-helix	109-126	18
α-helix	130-132	3
α-helix	134-136	3
α-helix	137-162	26
α-helix	180-203	24

Chain F: 42 helices, 62 β-strands

Element	Residues	Length	Sheet
α-helix	30-50	21
α-helix	54-63	10
β-strand	68-72	5	7
α-helix	77-109	33
α-helix	121	1
β-strand	124-126	3	8
β-strand	127-128	2	9
β-strand	144-146	3	8
β-strand	152-153	2	10
β-strand	160-161	2	10
β-strand	162	1	11
β-strand	167-168	2	9
β-strand	169	1	12
α-helix	179-187	9
α-helix	188-190	3
α-helix	192-201	10
β-strand	208-212	5	12
β-strand	217-220	4	12
β-strand	222	1	11
α-helix	240-242	3
α-helix	244-249	6
β-strand	255	1	13
β-strand	258-261	4	14
α-helix	264-266	3
α-helix	269-282	14
β-strand	290	1	13
β-strand	291	1	15
β-strand	293-296	4	14
β-strand	300-302	3	14
β-strand	310	1	15
α-helix	314-324	11
α-helix	335-345	11
β-strand	358	1	13
β-strand	359-364	6	14
α-helix	372-378	7
β-strand	385-391	7	14
α-helix	399-407	9
β-strand	411-415	5	14
α-helix	419-421	3
α-helix	429-432	4
α-helix	434-437	4
β-strand	447-448	2	12
β-strand	452-453	2	12
β-strand	460-469	10	12
β-strand	486-495	10	12
α-helix	496-500	5
β-strand	513-517	5	16
β-strand	522	1	17
β-strand	523-525	3	16
α-helix	533-535	3
β-strand	540	1	18
α-helix	543-545	3
β-strand	562	1	17
α-helix	563-565	3
α-helix	573-581	9
β-strand	586-592	7	16
α-helix	593-594	2
β-strand	595	1	19
α-helix	596	1
β-strand	602	1	19
β-strand	605-613	9	16
β-strand	621-626	6	16
β-strand	632-636	5	7
α-helix	641-648	8
α-helix	653-655	3
α-helix	656-659	4
β-strand	661-663	3	20
α-helix	674-675	2
α-helix	679-692	14
α-helix	702-718	17
α-helix	719-723	5
β-strand	732-734	3	20
β-strand	736-739	4	20
β-strand	744-746	3	20
α-helix	749-752	4
α-helix	765-772	8
β-strand	776	1	21
β-strand	777-779	3	20
α-helix	780-782	3
β-strand	795-800	6	20
β-strand	803-804	2	22
β-strand	809-810	2	22
β-strand	813-819	7	20
α-helix	821-829	9
β-strand	851-857	7	23
β-strand	861	1	24
β-strand	862-864	3	23
β-strand	877	1	24
α-helix	878-881	4
α-helix	883-891	9
β-strand	895-897	3	25
β-strand	900-907	8	26
α-helix	908-909	2
β-strand	910	1	18
β-strand	975-981	7	26
β-strand	984-986	3	25
β-strand	992-998	7	23
β-strand	1003-1010	8	23
α-helix	1011	1
β-strand	1014	1	21
β-strand	1016-1022	7	23
β-strand	1039-1041	3	26
α-helix	1046-1048	3
α-helix	1053-1055	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Voltage-dependent L-type calcium channel subunit alpha-1S	A	protein	1873	Oryctolagus cuniculus	P07293 (AlphaFold model)
Voltage-dependent calcium channel gamma-1 subunit	E	protein	222	Oryctolagus cuniculus	P19518 (AlphaFold model)
Voltage-dependent calcium channel subunit alpha-2/delta-1	F	protein	1105	Oryctolagus cuniculus	P13806 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7JPV_1 Voltage-dependent L-type calcium channel subunit alpha-1S (chains A)
MEPSSPQDEGLRKKQPKKPLPEVLPRPPRALFCLTLQNPLRKACISIVEWKPFETIILLT
IFANCVALAVYLPMPEDDNNSLNLGLEKLEYFFLTVFSIEAAMKIIAYGFLFHQDAYLRS
GWNVLDFIIVFLGVFTAILEQVNVIQSNTAPMSSKGAGLDVKALRAFRVLRPLRLVSGVP
SLQVVLNSIFKAMLPLFHIALLVLFMVIIYAIIGLELFKGKMHKTCYYIGTDIVATVENE
KPSPCARTGSGRPCTINGSECRGGWPGPNHGITHFDNFGFSMLTVYQCITMEGWTDVLYW
VNDAIGNEWPWIYFVTLILLGSFFILNLVLGVLSGEFTKEREKAKSRGTFQKLREKQQLE
EDLRGYMSWITQGEVMDVEDLREGKLSLEEGGSDTESLYEIEGLNKIIQFIRHWRQWNRV
FRWKCHDLVKSRVFYWLVILIVALNTLSIASEHHNQPLWLTHLQDIANRVLLSLFTIEML
LKMYGLGLRQYFMSIFNRFDCFVVCSGILELLLVESGAMTPLGISVLRCIRLLRLFKITK
YWTSLSNLVASLLNSIRSIASLLLLLFLFIIIFALLGMQLFGGRYDFEDTEVRRSNFDNF
PQALISVFQVLTGEDWNSVMYNGIMAYGGPSYPGVLVCIYFIILFVCGNYILLNVFLAIA
VDNLAEAESLTSAQKAKAEERKRRKMSRGLPDKTEEEKSVMAKKLEQKPKGEGIPTTAKL
KVDEFESNVNEVKDPYPSADFPGDDEEDEPEIPVSPRPRPLAELQLKEKAVPIPEASSFF
IFSPTNKVRVLCHRIVNATWFTNFILLFILLSSAALAAEDPIRAESVRNQILGYFDIAFT
SVFTVEIVLKMTTYGAFLHKGSFCRNYFNILDLLVVAVSLISMGLESSTISVVKILRVLR
VLRPLRAINRAKGLKHVVQCVFVAIRTIGNIVLVTTLLQFMFACIGVQLFKGKFFSCNDL
SKMTEEECRGYYYVYKDGDPTQMELRPRQWIHNDFHFDNVLSAMMSLFTVSTFEGWPQLL
YRAIDSNEEDMGPVYNNRVEMAIFFIIYIILIAFFMMNIFVGFVIVTFQEQGETEYKNCE
LDKNQRQCVQYALKARPLRCYIPKNPYQYQVWYVVTSSYFEYLMFALIMLNTICLGMQHY
HQSEEMNHISDILNVAFTIIFTLEMILKLLAFKARGYFGDPWNVFDFLIVIGSIIDVILS
EIDTFLASSGGLYCLGGGCGNVDPDESARISSAFFRLFRVMRLIKLLSRAEGVRTLLWTF
IKSFQALPYVALLIVMLFFIYAVIGMQMFGKIALVDGTQINRNNNFQTFPQAVLLLFRCA
TGEAWQEILLACSYGKLCDPESDYAPGEEYTCGTNFAYYYFISFYMLCAFLIINLFVAVI
MDNFDYLTRDWSILGPHHLDEFKAIWAEYDPEAKGRIKHLDVVTLLRRIQPPLGFGKFCP
HRVACKRLVGMNMPLNSDGTVTFNATLFALVRTALKIKTEGNFEQANEELRAIIKKIWKR
TSMKLLDQVIPPIGDDEVTVGKFYATFLIQEHFRKFMKRQEEYYGYRPKKDTVQIQAGLR
TIEEEAAPEIRRTISGDLTAEEELERAMVEAAMEERIFRRTGGLFGQVDTFLERTNSLPP
VMANQRPLQFAEIEMEELESPVFLEDFPQDARTNPLARANTNNANANVAYGNSNHSNNQM
FSSVHCEREFPGEAETPAAGRGALSHSHRALGPHSKPCAGKLNGQLVQPGMPINQAPPAP
CQQPSTDPPERGQRRTSLTGSLQDEAPQRRSSEGSTPRRPAPATALLIQEALVRGGLDTL
AADAGFVTATSQALADACQMEPEEVEVAATELLKARESVQGMASVPGSLSRRSSLGSLDQ
VQGSQETLIPPRP

Sequence of entity 2 (E), FASTA

>7JPV_2 Voltage-dependent calcium channel gamma-1 subunit (chains E)
MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSPHMENHNTTCEAAHFGLWRICTKR
IALGEDRSCGPITLPGEKNCSYFRHFNPGESSEIFEFTTQKEYSISAAAISVFSLGFLIM
GTICALMAFRKKRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIDSEDTVWIEYYYSW
SFACACAAFVLLFLGGISLLLFSLPRMPQNPWESCMDAEPEH

Sequence of entity 3 (F), FASTA

>7JPV_3 Voltage-dependent calcium channel subunit alpha-2/delta-1 (chains F)
MAAGRPLAWTLTLWQAWLILIGPSSEEPFPSAVTIKSWVDKMQEDLVTLAKTASGVHQLV
DIYEKYQDLYTVEPNNARQLVEIAARDIEKLLSNRSKALVRLALEAEKVQAAHQWREDFA
SNEVVYYNAKDDLDPEKNDSEPGSQRIKPVFIDDANFRRQVSYQHAAVHIPTDIYEGSTI
VLNELNWTSALDDVFKKNREEDPSLLWQVFGSATGLARYYPASPWVDNSRTPNKIDLYDV
RRRPWYIQGAASPKDMLILVDVSGSVSGLTLKLIRTSVSEMLETLSDDDFVNVASFNSNA
QDVSCFQHLVQANVRNKKVLKDAVNNITAKGITDYKKGFSFAFEQLLNYNVSRANCNKII
MLFTDGGEERAQEIFAKYNKDKKVRVFTFSVGQHNYDRGPIQWMACENKGYYYEIPSIGA
IRINTQEYLDVLGRPMVLAGDKAKQVQWTNVYLDALELGLVITGTLPVFNITGQFENKTN
LKNQLILGVMGVDVSLEDIKRLTPRFTLCPNGYYFAIDPNGYVLLHPNLQPKPIGVGIPT
INLRKRRPNVQNPKSQEPVTLDFLDAELENDIKVEIRNKMIDGESGEKTFRTLVKSQDER
YIDKGNRTYTWTPVNGTDYSLALVLPTYSFYYIKAKIEETITQARYSETLKPDNFEESGY
TFLAPRDYCSDLKPSDNNTEFLLNFNEFIDRKTPNNPSCNTDLINRVLLDAGFTNELVQN
YWSKQKNIKGVKARFVVTDGGITRVYPKEAGENWQENPETYEDSFYKRSLDNDNYVFTAP
YFNKSGPGAYESGIMVSKAVEIYIQGKLLKPAVVGIKIDVNSWIENFTKTSIRDPCAGPV
CDCKRNSDVMDCVILDDGGFLLMANHDDYTNQIGRFFGEIDPSLMRHLVNISVYAFNKSY
DYQSVCEPGAAPKQGAGHRSAYVPSIADILQIGWWATAAAWSILQQFLLSLTFPRLLEAA
DMEDDDFTASMSKQSCITEQTQYFFDNDSKSFSGVLDCGNCSRIFHVEKLMNTNLIFIMV
ESKGTCPCDTRLLIQAEQTSDGPDPCDMVKQPRYRKGPDVCFDNNVLEDYTDCGGVSGLN
PSLWSIIGIQFVLLWLVSGSRHCLL

Ligands and cofactors

ID	Name	Formula	Copies
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	1
3PE	1,2-Distearoyl-sn-glycerophosphoethanolamine	C41 H82 N O8 P	9
CA	Calcium ion	Ca	1

Primary citation

Structural Basis of the Modulation of the Voltage-Gated Calcium Ion Channel Ca v 1.1 by Dihydropyridine Compounds*. Gao, S., Yan, N. Angew Chem Int Ed Engl (2021) 60:3131-3137. DOI 10.1002/anie.202011793 · PubMed

Other PDB entries of the same protein (UniProt P07293 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7RXQ 2.03 Å, Crystal structure of junctophilin-2 in complex with a CaV1.1 peptide
1T3L 2.2 Å, Structural Analysis of the Voltage-Dependent Calcium Channel Beta Subunit Functional…
6JPA 2.6 Å, Rabbit Cav1.1-Verapamil Complex
6JP8 2.7 Å, Rabbit Cav1.1-Bay K8644 Complex
8E56 2.8 Å, Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone at 2.8…
8E57 2.8 Å, Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone and 100…
6JP5 2.9 Å, Rabbit Cav1.1-Nifedipine Complex
6JPB 2.9 Å, Rabbit Cav1.1-Diltiazem Complex
7JPX 2.9 Å, Rabbit Cav1.1 in the presence of 100 micromolar amlodipine in nanodiscs at 2.9 Angstrom…
7JPK 3.0 Å, Rabbit Cav1.1 in the presence of 100 micromolar (S)-(-)-Bay K8644 in nanodiscs at 3.0…
8E58 3.0 Å, Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone and 1…
7JPW 3.2 Å, Rabbit Cav1.1 in the presence of 100 micromolar (R)-(+)-Bay K8644 in nanodiscs at 3.2…

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