7JPW: PDB entry 7JPW

Rabbit Cav1.1 in the presence of 100 micromolar (R)-(+)-Bay K8644 in nanodiscs at 3.2 Angstrom resolution. Determined by electron microscopy at 3.2 Å resolution. Released 18 Nov 2020.

Method
Electron microscopy
Resolution
3.2 Å
Organism
Oryctolagus cuniculus
Chains
3
Atoms
18,583
Mol. weight
370.32 kDa
Ligands
VFY, PC1, 3PE, CA
Released
18 Nov 2020

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

Secondary structure: helices and β-sheets

7JPW contains 109 α-helices and 73 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: 67 helices, 12 β-strands

ElementResiduesLengthSheet
α-helix53-6917
α-helix75-773
α-helix81-877
α-helix90-10213
α-helix123-13917
α-helix162-17312
α-helix174-1785
α-helix181-1866
α-helix197-21721
β-strand225-22841
β-strand23411
α-helix252-2543
β-strand259-26241
α-helix278-28912
α-helix294-30512
α-helix311-3166
α-helix317-3248
α-helix325-34420
α-helix434-44916
α-helix458-48528
α-helix489-4913
α-helix496-4983
α-helix500-51112
α-helix521-5255
α-helix527-54014
α-helix549-55810
α-helix562-58019
α-helix600-61213
α-helix616-62611
α-helix632-6354
α-helix636-6383
α-helix639-6468
α-helix648-6558
α-helix665-6717
α-helix802-8054
α-helix806-8083
α-helix809-8179
α-helix827-84418
α-helix848-8514
α-helix869-88113
α-helix894-8985
α-helix899-9013
α-helix907-9104
α-helix915-9239
α-helix933-95018
β-strand955-95732
β-strand971-97553
α-helix976-9783
β-strand983-98753
β-strand990-99232
α-helix9931
α-helix1000-101112
α-helix1016-10249
α-helix1039-10413
α-helix1042-10498
α-helix1050-10567
α-helix1057-106812
α-helix1084-109411
β-strand109814
α-helix1106-111510
α-helix1118-113619
α-helix1152-117221
α-helix1181-120525
α-helix1237-12415
α-helix1242-12487
α-helix1251-126414
α-helix1268-128821
β-strand129215
α-helix1309-132113
α-helix1325-13306
β-strand133616
α-helix13371
β-strand133815
α-helix13391
β-strand135216
α-helix1357-138226
α-helix1384-13874
α-helix1396-140914
α-helix1425-14273
Chain E: 4 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix7-2519
β-strand34-3527
β-strand3618
β-strand48-5037
β-strand56-5947
β-strand80-8127
α-helix105-12622
α-helix137-16327
β-strand17518
α-helix181-20323
β-strand21714
Chain F: 38 helices, 54 β-strands
ElementResiduesLengthSheet
α-helix30-5223
α-helix54-6411
β-strand68-7259
α-helix77-10832
α-helix1211
β-strand124-125210
β-strand127-128211
β-strand144-145210
β-strand152-153212
β-strand160-161212
β-strand162113
β-strand167-169311
α-helix179-1879
α-helix188-1914
α-helix192-20110
β-strand208-212511
β-strand217-220411
β-strand222113
α-helix240-2423
α-helix244-2496
β-strand255-261714
α-helix264-2663
α-helix269-28214
β-strand290114
β-strand291115
β-strand293-296414
β-strand300-302314
β-strand310115
α-helix314-32411
α-helix335-34511
β-strand358-364714
α-helix372-3787
β-strand384-391814
α-helix399-4079
β-strand411-415514
α-helix419-4257
α-helix427-4304
α-helix434-4385
β-strand447-448211
β-strand452-453211
β-strand460-4691011
α-helix482-4843
β-strand486-4951011
α-helix496-4994
β-strand513-517516
β-strand523-525316
α-helix533-5353
β-strand540-541217
α-helix543-5453
α-helix572-58110
β-strand586-5951016
β-strand602-6131216
β-strand621-626616
β-strand632-63659
α-helix641-6499
α-helix653-6553
α-helix656-6594
β-strand662-664318
β-strand670119
α-helix679-69214
β-strand700119
α-helix702-72120
α-helix723-7253
β-strand732-734318
β-strand736-739418
β-strand743-746418
α-helix749-7535
α-helix761-7633
α-helix765-7728
β-strand776120
β-strand777-779318
β-strand795-800618
β-strand803-804221
β-strand809-810221
β-strand813-819718
α-helix821-8299
β-strand851-857722
β-strand861-864422
β-strand877122
α-helix878-8803
α-helix883-89210
β-strand895-9071323
β-strand910-911217
β-strand975-9861223
β-strand992-997622
β-strand1004-1010722
α-helix10111
β-strand1014120
β-strand1016-1022722
β-strand1039-1041323
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
>7JPW_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
>7JPW_2 Voltage-dependent calcium channel gamma-1 subunit (chains E)
MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSPHMENHNTTCEAAHFGLWRICTKR
IALGEDRSCGPITLPGEKNCSYFRHFNPGESSEIFEFTTQKEYSISAAAISVFSLGFLIM
GTICALMAFRKKRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIDSEDTVWIEYYYSW
SFACACAAFVLLFLGGISLLLFSLPRMPQNPWESCMDAEPEH
Sequence of entity 3 (F), FASTA
>7JPW_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
VFYmethyl (4R)-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropyrid…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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