6JPA: Rabbit Cav1.1-Verapamil Complex

Rabbit Cav1.1-Verapamil Complex. Determined by electron microscopy at 2.6 Å resolution. Released 12 Jun 2019.

Method
Electron microscopy
Resolution
2.6 Å
Organism
Oryctolagus cuniculus
Chains
5
Atoms
22,232
Mol. weight
437.88 kDa
Ligands
NAG, ETA, 4YH, 9Z9
Released
12 Jun 2019

Explore 6JPA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6JPA contains 130 α-helices and 88 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: 72 helices, 15 β-strands

ElementResiduesLengthSheet
α-helix45-484
α-helix53-6816
α-helix75-773
α-helix81-10020
α-helix110-1145
α-helix115-1195
α-helix121-14323
α-helix164-17310
α-helix174-1785
α-helix180-19213
α-helix194-1963
α-helix197-21822
β-strand226-22831
β-strand23411
α-helix252-2543
β-strand259-26131
α-helix278-28912
α-helix294-30512
α-helix310-3178
α-helix318-3247
α-helix325-34420
α-helix345-3495
α-helix350-37526
α-helix421-4299
α-helix434-4374
α-helix439-45113
α-helix458-48528
α-helix488-4936
α-helix495-51622
α-helix523-5297
α-helix530-54112
α-helix543-55816
α-helix560-58122
α-helix600-61213
α-helix616-62510
α-helix632-6365
α-helix638-67639
α-helix679-6868
α-helix791-7977
α-helix799-8057
α-helix809-8157
α-helix827-8315
α-helix833-85321
α-helix870-88213
α-helix893-8986
α-helix903-9053
α-helix912-92312
α-helix930-95021
β-strand955-95732
β-strand971-97553
β-strand983-98753
β-strand990-99232
α-helix1000-101112
α-helix1016-102510
α-helix1041-106828
α-helix1069-10735
α-helix1083-109412
β-strand109914
α-helix1106-111611
α-helix1118-113518
α-helix1144-117027
α-helix1181-120525
α-helix1235-12373
α-helix1240-12489
α-helix1251-126111
α-helix1268-128922
β-strand129215
α-helix1309-132012
α-helix1325-13317
β-strand133616
α-helix13371
β-strand133815
α-helix13391
α-helix1349-13513
β-strand135216
α-helix1357-138125
α-helix1384-13874
α-helix1396-140611
β-strand141214
β-strand1416-141727
α-helix1423-14264
α-helix1443-14508
β-strand1461-146227
α-helix1463-147412
α-helix1483-149210
α-helix1495-14962
α-helix1501-15055
Chain B: 4 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix79-9416
α-helix100-1012
β-strand103-10759
β-strand111110
β-strand12519
β-strand128110
β-strand133-13979
β-strand144-14969
β-strand156-16059
α-helix1611
α-helix162-1709
Chain C: 9 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand268-27149
α-helix2751
β-strand276-279411
α-helix288-30316
β-strand309-313511
α-helix344-35613
β-strand363-367511
α-helix375-3773
β-strand385-389511
α-helix394-4018
α-helix408-4103
α-helix412-42413
α-helix427-4293
β-strand432-434311
α-helix439-45719
Chain E: 4 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix8-2619
β-strand48-5038
β-strand56-5948
β-strand79-8138
α-helix105-12723
α-helix137-16428
α-helix182-20120
Chain F: 41 helices, 57 β-strands
ElementResiduesLengthSheet
α-helix30-378
α-helix42-5211
α-helix54-6411
β-strand68-72512
α-helix77-10832
β-strand124-125213
β-strand127-128214
β-strand144-145213
β-strand152115
β-strand161115
β-strand162116
β-strand167-169314
β-strand176117
β-strand178117
α-helix179-1879
α-helix188-1914
α-helix192-20110
β-strand208-212514
β-strand217-220414
β-strand222116
α-helix244-2507
β-strand254-261818
α-helix264-2663
α-helix269-28315
β-strand290-296718
β-strand300-302318
β-strand310118
α-helix314-32310
α-helix337-34610
β-strand357-364818
α-helix372-3787
β-strand385-391718
α-helix399-4079
β-strand411-415518
α-helix418-4203
α-helix429-4324
α-helix434-4374
α-helix440-4434
β-strand447-448214
α-helix449-4513
β-strand452-453214
β-strand460-4691014
β-strand486-4951014
α-helix496-4994
β-strand513-517519
β-strand522120
β-strand523-525319
α-helix533-5342
α-helix543-5453
β-strand562120
α-helix563-5664
α-helix574-5796
β-strand586-5951019
α-helix5961
β-strand602-6131219
β-strand621-627719
β-strand632-636512
α-helix641-6466
α-helix653-6553
β-strand661-662221
β-strand670122
α-helix679-69214
β-strand700122
α-helix702-71211
α-helix714-7185
α-helix719-7235
β-strand732-734323
β-strand737-739323
β-strand745-746221
α-helix751-7533
α-helix765-7728
β-strand776124
β-strand777-779323
α-helix780-7823
β-strand796-800523
β-strand803-804225
β-strand809-810225
β-strand813-819723
α-helix8201
α-helix821-8299
β-strand851-856626
β-strand861127
β-strand862-865426
β-strand877127
α-helix878-8803
α-helix883-8919
β-strand896-9071228
β-strand975-9851128
β-strand992-994326
β-strand997-998229
β-strand1003-1004229
β-strand1007-1010426
β-strand1014124
β-strand1017-1022626
α-helix1024-10263
β-strand1039-1040228
α-helix1046-10494
α-helix1053-10553

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Voltage-dependent L-type calcium channel subunit alpha-1SAprotein1506Oryctolagus cuniculusP07293 (AlphaFold model)
Voltage-dependent calcium channel gamma-1 subunitEprotein222Oryctolagus cuniculusP19518 (AlphaFold model)
Voltage-dependent L-type calcium channel subunit beta-1Bprotein450Oryctolagus cuniculusP19517 (AlphaFold model)
Voltage-dependent L-type calcium channel subunit beta-1Cprotein524Oryctolagus cuniculusP19517 (AlphaFold model)
Voltage-dependent calcium channel subunit alpha-2/delta-1Fprotein1046Oryctolagus cuniculusP13806 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>6JPA_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
TSMKLL
Sequence of entity 2 (E), FASTA
>6JPA_2 Voltage-dependent calcium channel gamma-1 subunit (chains E)
MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSPHMENHNTTCEAAHFGLWRICTKR
IALGEDRSCGPITLPGEKNCSYFRHFNPGESSEIFEFTTQKEYSISAAAISVFSLGFLIM
GTICALMAFRKKRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIDSEDTVWIEYYYSW
SFACACAAFVLLFLGGISLLLFSLPRMPQNPWESCMDAEPEH
Sequence of entity 3 (B), FASTA
>6JPA_3 Voltage-dependent L-type calcium channel subunit beta-1 (chains B)
QGPHMALRKEAERQALAQLEKAKTKPVAFAVRTNVGYNPSPGDEVPVEGVAITFEPKDFL
HIKEKYNNDWWIGRLVKEGCEVGFIPSPVKLDSLRLLQEQKLRQSRLSSSKSGDNSSSSL
GDVVTGTRRPTPPASGNEMTNLAFELEPLDLEEDEAELGEQSGSAKTSVSSVTTPPPHGT
RIPFFKKTEHVPPYDVVPSMRPIILVGPSLKGYEVTDMMQKALFDFLKHLFDGRISITRV
TADISLAKRSVLNNPSKHIIIERSNTRSSLAEVQSEIERIFELARTLQLVALDADTINHP
AQLSKTSLAPIIVYIKITSPKVLQRLIKSRGKSQSKHLNVQIAASEKLAQCPPEMFDIIL
DENQLEDACEHLAEYLEAYWKATHPPSSTPPNPLLNRTMATAALAASPAPVSNLQVQVLT
SLRRNLSFWGGLETSQRGGGAVPQQQEHAM
Sequence of entity 4 (C), FASTA
>6JPA_4 Voltage-dependent L-type calcium channel subunit beta-1 (chains C)
MVQKTSMSRGPYPPSQEIPMEVFDPSPQGKYSKRKGRFKRSDGSTSSDTTSNSFVRQGSA
ESYTSRPSDSDVSLEEDREALRKEAERQALAQLEKAKTKPVAFAVRTNVGYNPSPGDEVP
VEGVAITFEPKDFLHIKEKYNNDWWIGRLVKEGCEVGFIPSPVKLDSLRLLQEQKLRQSR
LSSSKSGDNSSSSLGDVVTGTRRPTPPASGNEMTNLAFELEPLDLEEDEAELGEQSGSAK
TSVSSVTTPPPHGTRIPFFKKTEHVPPYDVVPSMRPIILVGPSLKGYEVTDMMQKALFDF
LKHLFDGRISITRVTADISLAKRSVLNNPSKHIIIERSNTRSSLAEVQSEIERIFELART
LQLVALDADTINHPAQLSKTSLAPIIVYIKITSPKVLQRLIKSRGKSQSKHLNVQIAASE
KLAQCPPEMFDIILDENQLEDACEHLAEYLEAYWKATHPPSSTPPNPLLNRTMATAALAA
SPAPVSNLQVQVLTSLRRNLSFWGGLETSQRGGGAVPQQQEHAM
Sequence of entity 5 (F), FASTA
>6JPA_5 Voltage-dependent calcium channel subunit alpha-2/delta-1 (chains F)
FPSAVTIKSWVDKMQEDLVTLAKTASGVHQLVDIYEKYQDLYTVEPNNARQLVEIAARDI
EKLLSNRSKALVRLALEAEKVQAAHQWREDFASNEVVYYNAKDDLDPEKNDSEPGSQRIK
PVFIDDANFRRQVSYQHAAVHIPTDIYEGSTIVLNELNWTSALDDVFKKNREEDPSLLWQ
VFGSATGLARYYPASPWVDNSRTPNKIDLYDVRRRPWYIQGAASPKDMLILVDVSGSVSG
LTLKLIRTSVSEMLETLSDDDFVNVASFNSNAQDVSCFQHLVQANVRNKKVLKDAVNNIT
AKGITDYKKGFSFAFEQLLNYNVSRANCNKIIMLFTDGGEERAQEIFAKYNKDKKVRVFT
FSVGQHNYDRGPIQWMACENKGYYYEIPSIGAIRINTQEYLDVLGRPMVLAGDKAKQVQW
TNVYLDALELGLVITGTLPVFNITGQFENKTNLKNQLILGVMGVDVSLEDIKRLTPRFTL
CPNGYYFAIDPNGYVLLHPNLQPKPIGVGIPTINLRKRRPNVQNPKSQEPVTLDFLDAEL
ENDIKVEIRNKMIDGESGEKTFRTLVKSQDERYIDKGNRTYTWTPVNGTDYSLALVLPTY
SFYYIKAKIEETITQARYSETLKPDNFEESGYTFLAPRDYCSDLKPSDNNTEFLLNFNEF
IDRKTPNNPSCNTDLINRVLLDAGFTNELVQNYWSKQKNIKGVKARFVVTDGGITRVYPK
EAGENWQENPETYEDSFYKRSLDNDNYVFTAPYFNKSGPGAYESGIMVSKAVEIYIQGKL
LKPAVVGIKIDVNSWIENFTKTSIRDPCAGPVCDCKRNSDVMDCVILDDGGFLLMANHDD
YTNQIGRFFGEIDPSLMRHLVNISVYAFNKSYDYQSVCEPGAAPKQGAGHRSAYVPSIAD
ILQIGWWATAAAWSILQQFLLSLTFPRLLEAADMEDDDFTASMSKQSCITEQTQYFFDND
SKSFSGVLDCGNCSRIFHVEKLMNTNLIFIMVESKGTCPCDTRLLIQAEQTSDGPDPCDM
VKQPRYRKGPDVCFDNNVLEDYTDCG

Ligands and cofactors

IDNameFormulaCopies
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O68
ETAEthanolamineC2 H7 N O1
4YH(2S)-2-(3,4-dimethoxyphenyl)-5-{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino}-2-…C27 H38 N2 O42
9Z9(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-enC34 H56 O51
PC11,2-diacyl-sn-glycero-3-phosphocholineC44 H88 N O8 P2
3PE1,2-Distearoyl-sn-glycerophosphoethanolamineC41 H82 N O8 P8
CACalcium ionCa3

Primary citation

Molecular Basis for Ligand Modulation of a Mammalian Voltage-Gated Ca2+Channel. Zhao, Y., Huang, G., Wu, J. et al. Cell (2019) 177:1495-1506.e12. DOI 10.1016/j.cell.2019.04.043 · PubMed

Other PDB entries of the same protein (UniProt P07293 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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