7JPX: PDB entry 7JPX

Rabbit Cav1.1 in the presence of 100 micromolar amlodipine in nanodiscs at 2.9 Angstrom resolution. Determined by electron microscopy at 2.9 Å resolution. Released 18 Nov 2020.

Method
Electron microscopy
Resolution
2.9 Å
Organism
Oryctolagus cuniculus
Chains
3
Atoms
18,640
Mol. weight
371.14 kDa
Ligands
6UB, POV, PC1, 3PE
Released
18 Nov 2020

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

Secondary structure: helices and β-sheets

7JPX contains 106 α-helices and 63 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: 65 helices, 11 β-strands

ElementResiduesLengthSheet
α-helix46-494
α-helix57-604
α-helix63-697
α-helix71-733
α-helix81-9616
α-helix123-14220
α-helix164-1707
α-helix173-1764
α-helix180-19112
α-helix197-21721
β-strand225-22841
β-strand23411
α-helix252-2543
β-strand259-26241
α-helix278-28912
α-helix294-30512
α-helix311-3177
α-helix318-3236
α-helix324-34421
α-helix435-4384
α-helix446-4505
α-helix458-48427
α-helix488-4914
α-helix495-4973
α-helix500-51314
α-helix523-5308
α-helix531-5366
α-helix537-5415
α-helix545-58036
α-helix600-61213
α-helix616-62611
α-helix634-6374
α-helix638-65518
α-helix666-6727
α-helix799-81719
α-helix827-84519
α-helix868-88114
α-helix894-8985
α-helix904-9063
α-helix912-92110
α-helix930-95021
β-strand955-95732
β-strand971-97553
α-helix976-9783
β-strand983-98753
β-strand990-99232
α-helix1000-101112
α-helix1016-10249
α-helix1039-10413
α-helix1042-10487
α-helix1049-10568
α-helix1057-10604
α-helix1062-10654
α-helix1083-109412
α-helix1106-111510
α-helix1118-113619
α-helix1146-117227
α-helix1181-120121
α-helix1202-12043
α-helix1235-12384
α-helix1241-12488
α-helix1251-126515
α-helix1268-128821
β-strand129214
α-helix1309-132113
α-helix1325-13295
β-strand133615
α-helix13371
β-strand133814
α-helix13391
α-helix1344-13452
β-strand135215
α-helix1357-138125
α-helix1384-13874
α-helix1396-140914
α-helix1419-14257
Chain E: 4 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix7-2822
β-strand34-3636
β-strand49-5026
β-strand56-5836
β-strand79-8136
α-helix106-12722
α-helix137-16226
β-strand175-17736
α-helix181-20323
Chain F: 37 helices, 47 β-strands
ElementResiduesLengthSheet
α-helix30-5223
α-helix54-629
β-strand68-7257
α-helix75-10935
β-strand124-12638
β-strand127-12829
β-strand144-14638
β-strand152-153210
β-strand160-161210
β-strand162111
β-strand167-16939
α-helix179-1879
α-helix188-1903
α-helix192-20110
β-strand208-21259
β-strand217-22049
β-strand222111
α-helix240-2423
α-helix244-2507
β-strand255-261712
α-helix264-2663
α-helix269-28214
β-strand290-296712
β-strand300-302312
β-strand310112
α-helix314-32411
α-helix335-34511
β-strand358-364712
α-helix372-3787
β-strand385-391712
α-helix399-4079
β-strand411-415512
α-helix418-4203
α-helix421-4244
α-helix434-4374
α-helix440-4434
β-strand447-44829
β-strand452-45329
β-strand460-469109
β-strand486-495109
α-helix496-4994
β-strand513-517513
β-strand522114
β-strand523-525313
α-helix533-5353
β-strand540-541215
α-helix543-5453
β-strand562114
α-helix563-5653
α-helix572-58110
β-strand586-5951013
β-strand602-6131213
β-strand621-626613
β-strand632-63657
α-helix641-65010
α-helix653-6553
α-helix656-6594
β-strand661-664416
α-helix679-69214
α-helix702-71817
α-helix719-7235
β-strand732-739816
β-strand743-746416
α-helix765-7728
β-strand777-779316
α-helix780-7823
β-strand795-8041016
β-strand809-8191116
α-helix821-8288
β-strand851-857717
β-strand861-864417
β-strand877117
α-helix878-8803
α-helix883-89210
β-strand896-9071218
β-strand910-911215
β-strand975-9851118
β-strand992-998717
β-strand1003-1010817
α-helix10111
β-strand1016-1022717
β-strand1039-1041318
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
>7JPX_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
>7JPX_2 Voltage-dependent calcium channel gamma-1 subunit (chains E)
MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSPHMENHNTTCEAAHFGLWRICTKR
IALGEDRSCGPITLPGEKNCSYFRHFNPGESSEIFEFTTQKEYSISAAAISVFSLGFLIM
GTICALMAFRKKRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIDSEDTVWIEYYYSW
SFACACAAFVLLFLGGISLLLFSLPRMPQNPWESCMDAEPEH
Sequence of entity 3 (F), FASTA
>7JPX_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
6UBamlodipineC20 H25 Cl N2 O51
POV(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…C42 H82 N O8 P1
PC11,2-diacyl-sn-glycero-3-phosphocholineC44 H88 N O8 P1
3PE1,2-Distearoyl-sn-glycerophosphoethanolamineC41 H82 N O8 P9
CACalcium ionCa1

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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