5GJV: PDB entry 5GJV

Structure of the mammalian voltage-gated calcium channel Cav1.1 complex at near atomic resolution. Determined by electron microscopy at 3.6 Å resolution. Released 14 Sept 2016.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Oryctolagus cuniculus
Chains: 5
Atoms: 21,904
Mol. weight: 413.26 kDa
Ligands: PC1, NAG, CA
Released: 14 Sept 2016

Explore 5GJV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5GJV contains 122 α-helices and 78 β-strands across 5 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: 69 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	42-48	7
α-helix	53-67	15
α-helix	82-107	26
α-helix	110-112	3
α-helix	116-119	4
α-helix	121-138	18
α-helix	167-170	4
α-helix	172-178	7
α-helix	182-190	9
α-helix	197-218	22
β-strand	227	1	1
β-strand	228	1	2
α-helix	233	1
β-strand	234	1	1
α-helix	235	1
β-strand	259	1	2
α-helix	278-284	7
α-helix	286-289	4
α-helix	294-304	11
α-helix	311-335	25
α-helix	337-340	4
α-helix	341-343	3
α-helix	347-374	28
α-helix	420-427	8
α-helix	433-448	16
α-helix	459-484	26
α-helix	488-493	6
α-helix	495-516	22
α-helix	521-531	11
α-helix	532-540	9
α-helix	545-556	12
α-helix	562-580	19
α-helix	602-611	10
α-helix	616-627	12
α-helix	635-637	3
α-helix	640-650	11
α-helix	655-662	8
α-helix	666-668	3
α-helix	789-796	8
α-helix	799-817	19
α-helix	827-851	25
α-helix	856-860	5
α-helix	862-884	23
α-helix	895-898	4
α-helix	899-902	4
α-helix	904-908	5
α-helix	913-949	37
β-strand	955-957	3	3
β-strand	971-975	5	4
β-strand	983-987	5	4
β-strand	990-992	3	3
α-helix	1000-1009	10
α-helix	1016-1024	9
α-helix	1039-1042	4
α-helix	1044-1072	29
α-helix	1084-1092	9
α-helix	1106-1115	10
α-helix	1118-1124	7
α-helix	1126-1136	11
α-helix	1144-1172	29
α-helix	1181-1203	23
α-helix	1230-1233	4
α-helix	1237-1240	4
α-helix	1241-1245	5
α-helix	1251-1263	13
α-helix	1267-1288	22
α-helix	1309-1320	12
α-helix	1325-1331	7
α-helix	1358-1382	25
α-helix	1384-1387	4
α-helix	1396-1409	14
β-strand	1417-1418	2	5
α-helix	1422-1427	6
α-helix	1444-1450	7
α-helix	1457-1459	3
β-strand	1460-1461	2	5
α-helix	1463-1472	10
α-helix	1482-1497	16
α-helix	1505-1513	9

Chain B: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	78-80	3
α-helix	81-95	15
α-helix	100-101	2
β-strand	103-107	5	6
β-strand	111	1	7
α-helix	115-117	3
β-strand	125	1	6
β-strand	128	1	7
β-strand	133-139	7	6
β-strand	144-149	6	6
β-strand	157-160	4	6
α-helix	162-173	12

Chain C: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	268-271	4	6
α-helix	275-276	2
β-strand	277-280	4	8
α-helix	288-304	17
β-strand	309-314	6	8
α-helix	318-320	3
α-helix	344-357	14
β-strand	363-368	6	8
α-helix	374-376	3
β-strand	385-389	5	8
α-helix	394-403	10
α-helix	406-409	4
α-helix	412-424	13
α-helix	427-429	3
β-strand	432-434	3	8
α-helix	439-457	19

Chain E: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	7-28	22
β-strand	33-36	4	9
β-strand	48-50	3	9
β-strand	56-59	4	9
β-strand	78-81	4	9
α-helix	106-128	23
α-helix	137-164	28
β-strand	175-178	4	9
α-helix	180-203	24

Chain F: 33 helices, 50 β-strands

Element	Residues	Length	Sheet
α-helix	32-53	22
α-helix	56-65	10
β-strand	73-74	2	10
α-helix	78-111	34
β-strand	152-154	3	11
β-strand	159-161	3	11
β-strand	167-169	3	12
α-helix	181-187	7
α-helix	188-190	3
α-helix	191-201	11
β-strand	208-211	4	12
β-strand	217-219	3	12
α-helix	240-242	3
β-strand	254-255	2	13
β-strand	258-261	4	14
α-helix	269-281	13
α-helix	282-284	3
β-strand	290	1	13
β-strand	293-296	4	14
β-strand	300-301	2	14
α-helix	316-323	8
α-helix	324-326	3
α-helix	336-345	10
β-strand	357-358	2	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	421-424	4
α-helix	428-432	5
α-helix	434-437	4
β-strand	447-453	7	12
β-strand	460-469	10	12
β-strand	486-495	10	12
α-helix	496-500	5
β-strand	513	1	15
β-strand	516	1	15
β-strand	517-518	2	16
β-strand	522-523	2	16
β-strand	562	1	16
α-helix	563-566	4
α-helix	573-580	8
β-strand	586-595	10	15
β-strand	602-613	12	15
β-strand	621-627	7	15
β-strand	632-633	2	10
α-helix	634-636	3
α-helix	643-650	8
α-helix	653-655	3
β-strand	661-664	4	17
α-helix	679-693	15
α-helix	704-718	15
α-helix	719-723	5
β-strand	733	1	17
β-strand	736-739	4	17
β-strand	743-746	4	17
α-helix	751-754	4
α-helix	767-772	6
β-strand	776	1	18
β-strand	779	1	17
β-strand	795-800	6	17
β-strand	803	1	19
β-strand	810	1	19
β-strand	813-819	7	17
α-helix	821-830	10
β-strand	853-856	4	20
β-strand	861	1	21
β-strand	862-865	4	20
β-strand	877	1	21
α-helix	878-880	3
α-helix	883-891	9
β-strand	896-902	7	22
β-strand	906-907	2	23
β-strand	975-976	2	23
β-strand	978-985	8	22
β-strand	993-998	6	20
β-strand	1003-1011	9	20
β-strand	1014	1	18
β-strand	1016-1021	6	20
α-helix	1027-1028	2
β-strand	1038-1041	4	22
α-helix	1046-1049	4

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 L-type calcium channel subunit beta-1	B	protein	106	Oryctolagus cuniculus	P19517 (AlphaFold model)
Voltage-dependent L-type calcium channel subunit beta-1	C	protein	199	Oryctolagus cuniculus	P19517 (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	1106	Oryctolagus cuniculus	P13806 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5GJV_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 (B), FASTA

>5GJV_2 Voltage-dependent L-type calcium channel subunit beta-1 (chains B)
SLEVLFQGPHMALRKEAERQALAQLEKAKTKPVAFAVRTNVGYNPSPGDEVPVEGVAITF
EPKDFLHIKEKYNNDWWIGRLVKEGCEVGFIPSPVKLDSLRLLQEQ

Sequence of entity 3 (C), FASTA

>5GJV_3 Voltage-dependent L-type calcium channel subunit beta-1 (chains C)
VPPYDVVPSMRPIILVGPSLKGYEVTDMMQKALFDFLKHLFDGRISITRVTADISLAKRS
VLNNPSKHIIIERSNTRSSLAEVQSEIERIFELARTLQLVALDADTINHPAQLSKTSLAP
IIVYIKITSPKVLQRLIKSRGKSQSKHLNVQIAASEKLAQCPPEMFDIILDENQLEDACE
HLAEYLEAYWKATHPPSST

Sequence of entity 4 (E), FASTA

>5GJV_4 Voltage-dependent calcium channel gamma-1 subunit (chains E)
MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSPHMENHNTTCEAAHFGLWRICTKR
IALGEDRSCGPITLPGEKNCSYFRHFNPGESSEIFEFTTQKEYSISAAAISVFSLGFLIM
GTICALMAFRKKRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIDSEDTVWIEYYYSW
SFACACAAFVLLFLGGISLLLFSLPRMPQNPWESCMDAEPEH

Sequence of entity 5 (F), FASTA

>5GJV_5 Voltage-dependent calcium channel subunit alpha-2/delta-1 (chains F)
MAAGRPLAWTLTLWQAWLILIGPSSEEPFPSAVTIKSWVDKMQEDLVTLAKTASGVHQLV
DIYEKYQDLYTVEPNNARQLVEIAARDIEKLLSNRSKALVRLALEAEKVQAAHQWREDFA
SNEVVYYNAKDDLDPEKNDSEPGSQRIKPVFIDDANFRRQVSYQHAAVHIPTDIYEGSTI
VLNELNWTSALDDVFKKNREEDPSLLWQVFGSATGLARYYPASPWVDNSRTPNKIDLYDV
RRRPWYIQGAASPKDMLILVDVSGSVSGLTLKLIRTSVSEMLETLSDDDFVNVASFNSNA
QDVSCFQHLVQANVRNKKVLKDAVNNITAKGITDYKKGFSFAFEQLLNYNVSRANCNKII
MLFTDGGEERAQEIFAKYNKDKKVRVFTFSVGQHNYDRGPIQWMACENKGYYYEIPSIGA
IRINTQEYLDVLGRPMVLAGDKAKQVQWTNVYLDALELGLVITGTLPVFNITGQFENKTN
LKNQLILGVMGVDVSLEDIKRLTPRFTLCPNGYYFAIDPNGYVLLHPNLQPKPIGVGIPT
INLRKRRPNVQNPKSQEPVTLDFLDAELENDIKVEIRNKMIDGESGEKTFRTLVKSQDER
YIDKGNRTYTWTPVNGTDYSSLALVLPTYSFYYIKAKIEETITQARYSETLKPDNFEESG
YTFLAPRDYCSDLKPSDNNTEFLLNFNEFIDRKTPNNPSCNTDLINRVLLDAGFTNELVQ
NYWSKQKNIKGVKARFVVTDGGITRVYPKEAGENWQENPETYEDSFYKRSLDNDNYVFTA
PYFNKSGPGAYESGIMVSKAVEIYIQGKLLKPAVVGIKIDVNSWIENFTKTSIRDPCAGP
VCDCKRNSDVMDCVILDDGGFLLMANHDDYTNQIGRFFGEIDPSLMRHLVNISVYAFNKS
YDYQSVCEPGAAPKQGAGHRSAYVPSIADILQIGWWATAAAWSILQQFLLSLTFPRLLEA
ADMEDDDFTASMSKQSCITEQTQYFFDNDSKSFSGVLDCGNCSRIFHVEKLMNTNLIFIM
VESKGTCPCDTRLLIQAEQTSDGPDPCDMVKQPRYRKGPDVCFDNNVLEDYTDCXGVSGL
NPSLWSIIGIQFVLLWLVSGSRHCLL

Ligands and cofactors

ID	Name	Formula	Copies
PC1	1,2-diacyl-sn-glycero-3-phosphocholine	C44 H88 N O8 P	14
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8
CA	Calcium ion	Ca	3

Primary citation

Structure of the voltage-gated calcium channel Cav1.1 at 3.6 angstrom resolution. Wu, J.P., Yan, Z., Li, Z.Q. et al. Nature (2016) 537:191-196. DOI 10.1038/nature19321 · 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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5GJV is part of these collections:

Ion channels

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