8E58: PDB entry 8E58

Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone and 1 mM MNI-1 at 3.0 Angstrom resolution. Determined by electron microscopy at 3.0 Å resolution. Released 7 Dec 2022.

Method
Electron microscopy
Resolution
3.0 Å
Organism
Oryctolagus cuniculus
Chains
3
Atoms
18,449
Mol. weight
368.8 kDa
Ligands
CA, BBI, WFR, NAG
Released
7 Dec 2022

Explore 8E58 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E58 contains 111 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: 62 helices, 14 β-strands

ElementResiduesLengthSheet
α-helix54-6916
α-helix81-10727
α-helix124-14219
α-helix162-1709
α-helix172-1787
α-helix180-19112
α-helix194-1963
α-helix197-21721
β-strand225-22841
β-strand23411
β-strand259-26241
α-helix278-28912
α-helix294-30512
α-helix311-3188
α-helix319-3246
α-helix325-34521
α-helix434-44916
α-helix458-48528
α-helix490-4934
α-helix495-51218
α-helix513-5153
α-helix521-5299
α-helix530-5356
α-helix536-5405
α-helix546-5549
α-helix556-58126
α-helix600-61213
α-helix616-62611
α-helix635-6373
α-helix638-65215
α-helix653-6575
α-helix658-67114
α-helix799-81719
α-helix827-85024
α-helix869-88113
α-helix899-9024
α-helix904-9063
α-helix907-9104
α-helix912-92716
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-helix1057-107115
α-helix1084-109411
β-strand109814
α-helix1106-111611
α-helix1118-113619
α-helix1150-117223
α-helix1181-120525
α-helix1234-12374
α-helix1240-12434
α-helix1245-12495
α-helix1251-126616
α-helix1270-128920
β-strand129215
β-strand130116
β-strand130416
α-helix1309-132012
α-helix1325-13306
β-strand133617
α-helix13371
β-strand133815
α-helix13391
β-strand135217
α-helix1357-138226
α-helix1384-13874
α-helix1396-140813
α-helix1419-142810
Chain E: 5 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix7-2620
β-strand3318
β-strand49-5029
β-strand5118
β-strand56110
β-strand57-5829
β-strand81110
α-helix106-12924
α-helix130-1323
α-helix137-16428
α-helix182-20322
β-strand21714
Chain F: 44 helices, 52 β-strands
ElementResiduesLengthSheet
α-helix30-4819
α-helix49-535
α-helix54-6411
β-strand68-72511
α-helix75-10935
α-helix1211
β-strand124-125212
β-strand127-128213
α-helix135-1373
β-strand144-145212
β-strand152-153214
β-strand160-161214
β-strand162115
β-strand167-169313
α-helix179-1879
α-helix188-1903
α-helix191-20111
β-strand208-212513
β-strand217-220413
β-strand222115
α-helix240-2423
α-helix244-2507
β-strand254-261816
α-helix264-2663
α-helix269-28214
β-strand290-296716
β-strand300-302316
β-strand310116
α-helix314-32411
α-helix335-34612
β-strand357-364816
α-helix372-3787
β-strand385-391716
α-helix399-4057
β-strand411-415516
α-helix418-4203
α-helix421-4244
α-helix429-4324
α-helix434-4396
α-helix440-4434
β-strand447-448213
α-helix449-4513
β-strand452-453213
β-strand460-4691013
α-helix482-4843
β-strand486-4951013
α-helix496-5005
β-strand513-517517
β-strand522118
β-strand523-525317
α-helix533-5353
β-strand540-541219
α-helix543-5453
β-strand562118
α-helix571-58111
β-strand586-5951017
β-strand602-6131217
β-strand621-627717
β-strand632-636511
α-helix641-65010
α-helix653-6553
α-helix656-6594
β-strand661-664420
α-helix679-69214
α-helix702-71817
α-helix719-7235
β-strand732-739820
β-strand743-746420
α-helix749-7546
α-helix761-7633
α-helix765-7728
β-strand776121
β-strand777-779320
α-helix780-7823
β-strand795-800620
β-strand803-804222
β-strand809-810222
β-strand813-819720
α-helix821-8299
β-strand851-857723
β-strand861124
β-strand862-864323
β-strand877124
α-helix878-8803
α-helix883-89210
β-strand896-9071225
β-strand910-911219
β-strand975-9851125
β-strand992-997623
β-strand1004-1010723
α-helix10111
β-strand1014121
β-strand1016-1022723
β-strand1039-1041325
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-1Fprotein1106Oryctolagus cuniculusP13806 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8E58_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
>8E58_2 Voltage-dependent calcium channel gamma-1 subunit (chains E)
MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSPHMENHNTTCEAAHFGLWRICTKR
IALGEDRSCGPITLPGEKNCSYFRHFNPGESSEIFEFTTQKEYSISAAAISVFSLGFLIM
GTICALMAFRKKRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIDSEDTVWIEYYYSW
SFACACAAFVLLFLGGISLLLFSLPRMPQNPWESCMDAEPEH
Sequence of entity 3 (F), FASTA
>8E58_3 Voltage-dependent calcium channel subunit alpha-2/delta-1 (chains F)
MAAGRPLAWTLTLWQAWLILIGPSSEEPFPSAVTIKSWVDKMQEDLVTLAKTASGVHQLV
DIYEKYQDLYTVEPNNARQLVEIAARDIEKLLSNRSKALVRLALEAEKVQAAHQWREDFA
SNEVVYYNAKDDLDPEKNDSEPGSQRIKPVFIDDANFRRQVSYQHAAVHIPTDIYEGSTI
VLNELNWTSALDDVFKKNREEDPSLLWQVFGSATGLARYYPASPWVDNSRTPNKIDLYDV
RRRPWYIQGAASPKDMLILVDVSGSVSGLTLKLIRTSVSEMLETLSDDDFVNVASFNSNA
QDVSCFQHLVQANVRNKKVLKDAVNNITAKGITDYKKGFSFAFEQLLNYNVSRANCNKII
MLFTDGGEERAQEIFAKYNKDKKVRVFTFSVGQHNYDRGPIQWMACENKGYYYEIPSIGA
IRINTQEYLDVLGRPMVLAGDKAKQVQWTNVYLDALELGLVITGTLPVFNITGQFENKTN
LKNQLILGVMGVDVSLEDIKRLTPRFTLCPNGYYFAIDPNGYVLLHPNLQPKPIGVGIPT
INLRKRRPNVQNPKSQEPVTLDFLDAELENDIKVEIRNKMIDGESGEKTFRTLVKSQDER
YIDKGNRTYTWTPVNGTDYSSLALVLPTYSFYYIKAKIEETITQARYSETLKPDNFEESG
YTFLAPRDYCSDLKPSDNNTEFLLNFNEFIDRKTPNNPSCNTDLINRVLLDAGFTNELVQ
NYWSKQKNIKGVKARFVVTDGGITRVYPKEAGENWQENPETYEDSFYKRSLDNDNYVFTA
PYFNKSGPGAYESGIMVSKAVEIYIQGKLLKPAVVGIKIDVNSWIENFTKTSIRDPCAGP
VCDCKRNSDVMDCVILDDGGFLLMANHDDYTNQIGRFFGEIDPSLMRHLVNISVYAFNKS
YDYQSVCEPGAAPKQGAGHRSAYVPSIADILQIGWWATAAAWSILQQFLLSLTFPRLLEA
ADMEDDDFTASMSKQSCITEQTQYFFDNDSKSFSGVLDCGNCSRIFHVEKLMNTNLIFIM
VESKGTCPCDTRLLIQAEQTSDGPDPCDMVKQPRYRKGPDVCFDNNVLEDYTDCGGVSGL
NPSLWSIIGIQFVLLWLVSGSRHCLL

Ligands and cofactors

IDNameFormulaCopies
CACalcium ionCa2
BBI(2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methano…C25 H29 I2 N O31
WFRpropan-2-yl (2S)-2-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H…C24 H30 N3 O9 P1
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O67

Primary citation

Structural basis for the severe adverse interaction of sofosbuvir and amiodarone on L-type Ca v channels. Yao, X., Gao, S., Wang, J. et al. Cell (2022) 185:4801-4810.e13. DOI 10.1016/j.cell.2022.10.024 · 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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