7JPL: PDB entry 7JPL

Rabbit Cav1.1 in the presence of 10 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
18,565
Mol. weight
370.32 kDa
Ligands
C8U, PC1, 3PE, CA
Released
18 Nov 2020

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

Secondary structure: helices and β-sheets

7JPL contains 106 α-helices and 71 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: 66 helices, 15 β-strands

ElementResiduesLengthSheet
α-helix53-586
α-helix61-699
α-helix81-877
α-helix89-10618
α-helix124-14017
α-helix165-1706
α-helix172-1787
α-helix180-1867
α-helix197-21721
β-strand225-22841
β-strand23411
α-helix252-2543
β-strand259-26241
α-helix278-28912
α-helix294-30411
α-helix311-3188
α-helix319-3235
α-helix324-34219
α-helix434-4363
α-helix438-44912
α-helix458-47619
α-helix483-4864
α-helix497-51115
α-helix523-5297
α-helix532-5365
α-helix537-5404
α-helix543-5475
α-helix549-5557
α-helix562-58019
β-strand58212
β-strand59712
α-helix600-61112
α-helix616-62510
α-helix634-6374
α-helix638-6469
α-helix648-6558
α-helix658-6614
α-helix664-6729
α-helix799-81719
α-helix827-85226
α-helix871-88010
α-helix895-8984
α-helix903-9064
α-helix913-92715
α-helix934-94916
β-strand955-95623
β-strand971-97554
α-helix976-9783
β-strand983-98754
β-strand991-99223
α-helix1000-101112
α-helix1016-10238
α-helix1039-10435
α-helix1044-10507
α-helix1051-10566
α-helix1057-106711
α-helix1084-109310
α-helix1106-111611
α-helix1118-113518
α-helix1152-117221
α-helix1181-120323
α-helix1233-12364
α-helix1237-12404
α-helix1241-12488
α-helix1251-126515
α-helix1268-128821
β-strand129215
β-strand129616
β-strand129816
α-helix1309-132113
α-helix1325-13317
β-strand133617
α-helix13371
β-strand133815
α-helix13391
β-strand135217
α-helix1357-138125
α-helix1384-13874
α-helix1396-140914
α-helix1424-14285
α-helix1431-14333
Chain E: 4 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix7-2620
β-strand33-3538
β-strand48-5148
β-strand56-5948
β-strand79-8138
α-helix105-12622
α-helix137-16327
β-strand176-17728
α-helix182-20322
Chain F: 36 helices, 51 β-strands
ElementResiduesLengthSheet
α-helix30-5223
α-helix54-6411
β-strand68-7259
α-helix77-10933
β-strand124-125210
β-strand127-128211
β-strand144-145210
β-strand152-153212
β-strand160-161212
β-strand162113
β-strand167-169311
α-helix179-1879
α-helix188-1903
α-helix192-20110
β-strand208-212511
β-strand217-220411
β-strand222113
α-helix244-2496
β-strand254-261814
α-helix269-28214
β-strand290-296714
β-strand300-302314
β-strand310114
α-helix314-32411
α-helix335-34511
β-strand357-364814
α-helix372-3787
β-strand384-391814
α-helix399-4057
β-strand411-415514
α-helix421-4244
α-helix427-4293
α-helix434-4385
α-helix440-4434
β-strand447-448211
α-helix449-4513
β-strand452-453211
β-strand460-4691011
β-strand486-4951011
α-helix496-4994
β-strand513-517515
β-strand522116
β-strand523-525315
α-helix533-5353
α-helix543-5453
β-strand562116
α-helix572-5809
β-strand586-5951015
β-strand602-6131215
β-strand621-626615
β-strand632-63659
α-helix641-6499
α-helix653-6553
α-helix656-6594
β-strand661-663317
β-strand670118
α-helix679-69214
β-strand700118
α-helix702-71817
α-helix719-7235
β-strand732-734317
β-strand736-739417
β-strand744-746317
α-helix749-7524
α-helix761-7633
α-helix765-7728
β-strand777-779317
α-helix780-7823
β-strand795-800617
β-strand803-804219
β-strand809-810219
β-strand813-819717
α-helix821-8299
β-strand851-857720
β-strand861121
β-strand862-864320
β-strand877121
α-helix878-8803
α-helix883-8919
β-strand895-9071322
β-strand975-9861222
β-strand993-997520
β-strand1004-1011820
β-strand1016-1022720
β-strand1039-1041322
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
>7JPL_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
>7JPL_2 Voltage-dependent calcium channel gamma-1 subunit (chains E)
MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSPHMENHNTTCEAAHFGLWRICTKR
IALGEDRSCGPITLPGEKNCSYFRHFNPGESSEIFEFTTQKEYSISAAAISVFSLGFLIM
GTICALMAFRKKRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIDSEDTVWIEYYYSW
SFACACAAFVLLFLGGISLLLFSLPRMPQNPWESCMDAEPEH
Sequence of entity 3 (F), FASTA
>7JPL_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
C8Umethyl (4~{S})-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropy…C16 H15 F3 N2 O41
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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