6JPB: Rabbit Cav1.1-Diltiazem Complex

Rabbit Cav1.1-Diltiazem Complex. Determined by electron microscopy at 2.9 Å resolution. Released 12 Jun 2019.

Method
Electron microscopy
Resolution
2.9 Å
Organism
Oryctolagus cuniculus
Chains
5
Atoms
21,989
Mol. weight
473.15 kDa
Ligands
NAG, ETA, C9F, PC1
Released
12 Jun 2019

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

Secondary structure: helices and β-sheets

6JPB contains 142 α-helices and 83 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: 81 helices, 9 β-strands

ElementResiduesLengthSheet
α-helix40-434
α-helix44-485
α-helix52-6918
α-helix81-844
α-helix87-10014
α-helix114-1196
α-helix122-14221
α-helix164-1663
α-helix168-1703
α-helix174-1785
α-helix183-1864
α-helix190-1923
α-helix197-20711
α-helix209-21810
β-strand225-22841
α-helix2331
β-strand23411
α-helix2351
α-helix252-2543
β-strand259-26241
α-helix278-28912
α-helix294-3018
α-helix311-3188
α-helix319-3235
α-helix325-33612
α-helix342-3454
α-helix352-37120
α-helix421-4299
α-helix439-44911
α-helix458-48427
α-helix488-4936
α-helix497-51317
α-helix523-5308
α-helix531-54111
α-helix548-5536
α-helix560-5634
α-helix565-58016
α-helix601-61111
α-helix616-62611
α-helix634-6396
α-helix640-64910
α-helix656-68631
α-helix789-7957
α-helix799-8068
α-helix813-8175
α-helix827-83913
α-helix842-85312
α-helix869-88113
α-helix895-8984
α-helix899-9024
α-helix905-9073
α-helix912-92615
α-helix928-9303
α-helix931-94919
β-strand955-95622
β-strand971-97553
α-helix976-9783
β-strand983-98753
β-strand991-99222
α-helix9931
α-helix1000-101213
α-helix1017-10248
α-helix1039-10424
α-helix1044-10485
α-helix1049-10568
α-helix1058-106710
α-helix1083-109311
α-helix1106-111510
α-helix1118-113619
α-helix1144-117027
α-helix1177-11793
α-helix1181-120424
α-helix1233-12386
α-helix1241-12488
α-helix1251-126515
α-helix1270-128819
β-strand129214
α-helix1309-132113
α-helix1325-13295
α-helix1330-13323
α-helix13371
β-strand133814
α-helix13391
α-helix1357-138024
α-helix1396-140914
α-helix1419-14268
α-helix1444-14507
α-helix1464-147411
α-helix1489-14924
α-helix1500-15034
Chain B: 4 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix79-9416
α-helix100-1012
β-strand103-10646
β-strand11117
β-strand12516
β-strand12817
β-strand133-13976
β-strand144-14966
β-strand156-16056
α-helix1611
α-helix162-17312
Chain C: 12 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand269-27136
α-helix2751
β-strand276-28058
α-helix288-2958
α-helix296-2983
α-helix300-3034
β-strand309-31358
α-helix344-35714
β-strand363-36758
α-helix374-3774
β-strand385-38958
α-helix394-4018
α-helix408-4103
α-helix412-4187
α-helix421-4244
α-helix427-4293
β-strand432-43438
α-helix439-45719
Chain E: 4 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix7-2620
β-strand3415
β-strand48-5145
β-strand56-5945
β-strand79-8135
α-helix106-12722
α-helix137-16327
α-helix182-20120
Chain F: 41 helices, 57 β-strands
ElementResiduesLengthSheet
α-helix30-378
α-helix42-5211
α-helix54-6411
β-strand68-7259
α-helix77-10832
β-strand124-125210
β-strand127-128211
β-strand144-145210
β-strand152112
β-strand161112
β-strand162113
β-strand167-169311
β-strand176114
β-strand178114
α-helix179-1879
α-helix188-1914
α-helix192-20110
β-strand208-212511
β-strand217-220411
β-strand222113
α-helix244-2507
β-strand254-261815
α-helix264-2663
α-helix269-28315
β-strand290-296715
β-strand300-302315
β-strand310115
α-helix314-32310
α-helix335-34612
β-strand357-364815
α-helix372-3787
β-strand385-391715
α-helix399-4079
β-strand411-415515
α-helix418-4203
α-helix429-4324
α-helix434-4374
α-helix440-4434
β-strand447-448211
α-helix449-4513
β-strand452-453211
β-strand460-4691011
β-strand486-4951011
α-helix496-4994
β-strand513-517516
β-strand522117
β-strand523-525316
α-helix533-5342
α-helix543-5453
β-strand562117
α-helix563-5664
α-helix574-5796
β-strand586-5951016
α-helix5961
β-strand602-6131216
β-strand621-627716
β-strand632-63659
α-helix641-6466
α-helix653-6553
β-strand661-662218
β-strand670119
α-helix679-69214
β-strand700119
α-helix702-71211
α-helix714-7185
α-helix719-7235
β-strand732-734320
β-strand737-739320
β-strand745-746218
α-helix751-7533
α-helix765-7728
β-strand776121
β-strand777-779320
α-helix780-7823
β-strand796-800520
β-strand803-804222
β-strand809-810222
β-strand813-819720
α-helix8201
α-helix821-8299
β-strand851-856623
β-strand861124
β-strand862-865423
β-strand877124
α-helix878-8803
α-helix883-8919
β-strand896-9071225
β-strand975-9851125
β-strand992-994323
β-strand997-998226
β-strand1003-1004226
β-strand1007-1010423
β-strand1014121
β-strand1017-1022623
α-helix1024-10263
β-strand1039-1040225
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 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
>6JPB_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
>6JPB_2 Voltage-dependent calcium channel gamma-1 subunit (chains E)
MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSPHMENHNTTCEAAHFGLWRICTKR
IALGEDRSCGPITLPGEKNCSYFRHFNPGESSEIFEFTTQKEYSISAAAISVFSLGFLIM
GTICALMAFRKKRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIDSEDTVWIEYYYSW
SFACACAAFVLLFLGGISLLLFSLPRMPQNPWESCMDAEPEH
Sequence of entity 3 (B), FASTA
>6JPB_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
>6JPB_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
>6JPB_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
C9FDiltiazemC22 H26 N2 O4 S1
PC11,2-diacyl-sn-glycero-3-phosphocholineC44 H88 N O8 P1
3PE1,2-Distearoyl-sn-glycerophosphoethanolamineC41 H82 N O8 P4
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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