7JPK: PDB entry 7JPK

Rabbit Cav1.1 in the presence of 100 micromolar (S)-(-)-Bay K8644 in nanodiscs at 3.0 Angstrom resolution. Determined by electron microscopy at 3.0 Å resolution. Released 18 Nov 2020.

Method
Electron microscopy
Resolution
3.0 Å
Organism
Oryctolagus cuniculus
Chains
3
Atoms
18,591
Mol. weight
370.32 kDa
Ligands
CA, PC1, C8U, 3PE
Released
18 Nov 2020

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

Secondary structure: helices and β-sheets

7JPK contains 106 α-helices and 67 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, 11 β-strands

ElementResiduesLengthSheet
α-helix54-6916
α-helix81-855
α-helix93-10513
α-helix124-14017
α-helix164-1696
α-helix171-1733
α-helix174-1785
α-helix180-19213
α-helix197-21822
β-strand225-22841
β-strand23411
α-helix252-2543
β-strand259-26241
α-helix278-28912
α-helix294-30512
α-helix311-3188
α-helix319-3246
α-helix325-34521
α-helix434-44916
α-helix458-4669
α-helix469-4779
α-helix481-4855
α-helix500-51415
α-helix521-5288
α-helix530-5345
α-helix536-5394
α-helix543-5475
α-helix549-58032
α-helix600-61213
α-helix616-62611
α-helix635-6373
α-helix638-66932
α-helix799-81719
α-helix829-84113
α-helix869-88113
α-helix893-8986
α-helix904-9063
α-helix907-9104
α-helix912-92514
α-helix930-95021
β-strand955-95732
β-strand971-97553
α-helix976-9783
β-strand983-98753
β-strand990-99232
α-helix1000-101112
α-helix1016-10238
α-helix1039-10413
α-helix1042-10487
α-helix1049-10568
α-helix1057-107115
α-helix1083-109412
α-helix1106-111510
α-helix1118-113518
α-helix1152-117221
α-helix1177-11793
α-helix1181-120424
α-helix1235-12373
α-helix1241-12488
α-helix1251-126616
α-helix1271-128818
β-strand129214
α-helix1309-132012
α-helix1325-13317
β-strand133615
α-helix13371
β-strand133814
α-helix13391
β-strand135215
α-helix1357-138125
α-helix1384-13874
α-helix1396-140914
α-helix1424-14285
Chain E: 5 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix7-2620
β-strand34-3636
β-strand48-5037
β-strand56-5947
β-strand79-8137
α-helix105-12723
α-helix134-1363
α-helix137-16226
β-strand175-17736
α-helix181-20323
Chain F: 39 helices, 51 β-strands
ElementResiduesLengthSheet
α-helix30-5223
α-helix54-629
β-strand68-7258
α-helix77-9519
α-helix97-10913
β-strand124-12529
β-strand127-128210
β-strand144-14529
β-strand152-153211
β-strand160-161211
β-strand162112
β-strand167-169310
α-helix184-1874
α-helix188-1903
α-helix192-20110
β-strand208-212510
β-strand217-220410
β-strand222112
α-helix240-2423
α-helix244-2507
β-strand255-261713
α-helix264-2663
α-helix269-28214
β-strand290-296713
β-strand300-302313
β-strand310113
α-helix314-32411
α-helix335-34511
β-strand358-364713
α-helix372-3787
β-strand384-391813
α-helix399-4079
β-strand411-415513
α-helix418-4203
α-helix421-4255
α-helix428-4325
α-helix434-4374
α-helix440-4434
β-strand447-448210
β-strand452-453210
β-strand460-4691010
α-helix4701
β-strand486-4951010
α-helix496-4994
β-strand513-517514
β-strand522115
β-strand523-525314
α-helix533-5353
β-strand540-541216
β-strand562115
α-helix563-5653
α-helix572-58110
β-strand586-5951014
β-strand602-6131214
β-strand621-626614
β-strand632-63658
α-helix641-6499
α-helix653-6553
α-helix656-6594
β-strand661-664417
α-helix679-69214
α-helix702-71817
α-helix719-7235
β-strand732-734317
β-strand736-739417
β-strand743-746417
α-helix749-7524
α-helix765-7728
β-strand777-779317
α-helix7801
β-strand795-800617
β-strand803-804218
β-strand809-810218
β-strand813-819717
α-helix821-8299
β-strand851-857719
β-strand861120
β-strand862-864319
β-strand877120
α-helix878-8803
α-helix883-8919
β-strand895-9071321
β-strand910-911216
β-strand975-9861221
β-strand992-997619
β-strand1004-1011819
β-strand1016-1022719
β-strand1039-1041321
α-helix1046-10494
α-helix1053-10553

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Voltage-dependent L-type calcium channel subunit alpha-1SAprotein1873Oryctolagus cuniculusP07293 (AlphaFold model)
Voltage-dependent calcium channel gamma-1 subunitEprotein222Oryctolagus cuniculusP19518 (AlphaFold model)
Voltage-dependent calcium channel subunit alpha-2/delta-1Fprotein1105Oryctolagus cuniculusP13806 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>7JPK_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
>7JPK_2 Voltage-dependent calcium channel gamma-1 subunit (chains E)
MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSPHMENHNTTCEAAHFGLWRICTKR
IALGEDRSCGPITLPGEKNCSYFRHFNPGESSEIFEFTTQKEYSISAAAISVFSLGFLIM
GTICALMAFRKKRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIDSEDTVWIEYYYSW
SFACACAAFVLLFLGGISLLLFSLPRMPQNPWESCMDAEPEH
Sequence of entity 3 (F), FASTA
>7JPK_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

IDNameFormulaCopies
CACalcium ionCa1
PC11,2-diacyl-sn-glycero-3-phosphocholineC44 H88 N O8 P1
C8Umethyl (4~{S})-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropy…C16 H15 F3 N2 O41
3PE1,2-Distearoyl-sn-glycerophosphoethanolamineC41 H82 N O8 P9

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:

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