8E56: PDB entry 8E56

Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone at 2.8 Angstrom resolution. Determined by electron microscopy at 2.8 Å resolution. Released 7 Dec 2022.

Method
Electron microscopy
Resolution
2.8 Å
Organism
Oryctolagus cuniculus
Chains
3
Atoms
18,461
Mol. weight
369.01 kDa
Ligands
CA, BBI, 3PE, NAG
Released
7 Dec 2022

Explore 8E56 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E56 contains 107 α-helices and 70 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: 59 helices, 14 β-strands

ElementResiduesLengthSheet
α-helix47-504
α-helix53-7018
α-helix81-10727
α-helix123-14018
α-helix162-17312
α-helix174-1785
α-helix180-19112
α-helix194-1963
α-helix197-21822
β-strand225-22841
β-strand23411
β-strand259-26241
α-helix278-28912
α-helix294-30512
α-helix310-3189
α-helix319-3246
α-helix325-34521
α-helix434-45017
α-helix458-48629
α-helix489-4935
α-helix498-51417
α-helix521-53212
α-helix533-5353
α-helix536-5394
α-helix544-5474
α-helix549-58133
α-helix600-61213
α-helix616-62611
α-helix632-6354
α-helix638-66932
α-helix799-81719
α-helix829-85123
α-helix869-88113
α-helix894-8974
α-helix899-9024
α-helix906-9105
α-helix912-92716
α-helix932-95019
β-strand955-95622
β-strand971-97553
α-helix976-9783
β-strand983-98753
β-strand991-99222
α-helix1000-101112
α-helix1016-10249
α-helix1039-10413
α-helix1042-10487
α-helix1049-10557
α-helix1056-107116
α-helix1084-109310
β-strand109814
α-helix1106-111611
α-helix1118-113619
α-helix1149-117224
α-helix1181-120525
α-helix1235-12373
α-helix1240-12489
α-helix1251-126515
α-helix1270-128819
β-strand129215
β-strand130116
β-strand130416
α-helix1309-132113
α-helix1325-13306
β-strand133617
α-helix13371
β-strand133815
α-helix13391
β-strand135217
α-helix1356-138227
α-helix1384-13874
α-helix1396-140914
α-helix1419-142810
Chain E: 6 helices, 6 β-strands
ElementResiduesLengthSheet
α-helix2-54
α-helix7-2822
β-strand33-3648
β-strand48-5148
β-strand56-5948
β-strand79-8138
α-helix105-12824
α-helix134-1363
α-helix137-16226
β-strand175-17738
α-helix181-20323
β-strand21714
Chain F: 42 helices, 50 β-strands
ElementResiduesLengthSheet
α-helix30-5223
α-helix54-6411
β-strand68-7259
α-helix75-10834
α-helix1211
β-strand124-125210
β-strand127-128211
β-strand144-145210
β-strand152-154312
β-strand159-161312
β-strand162113
β-strand167-169311
α-helix179-18810
α-helix191-20111
β-strand208-212511
β-strand217-220411
β-strand222113
α-helix240-2423
α-helix244-2507
β-strand255-261714
α-helix264-2663
α-helix269-28214
β-strand290-296714
β-strand300-302314
β-strand310114
α-helix314-32411
α-helix335-34612
β-strand358-364714
α-helix372-3787
β-strand385-391714
α-helix399-4057
β-strand411-415514
α-helix418-4203
α-helix421-4244
α-helix428-4325
α-helix434-4396
α-helix440-4434
β-strand447-448211
β-strand452-453211
β-strand460-4691011
β-strand486-4951011
α-helix496-5005
β-strand513-517515
β-strand522116
β-strand523-525315
α-helix533-5353
β-strand540-541217
α-helix543-5453
β-strand562116
α-helix563-5653
α-helix571-58111
β-strand586-5951015
β-strand602-6131215
β-strand621-626615
α-helix628-6303
β-strand632-63659
α-helix641-6499
α-helix653-6553
α-helix656-6594
β-strand661-664418
α-helix679-69214
α-helix702-71817
α-helix719-7235
β-strand732-739818
β-strand743-746418
α-helix749-7524
α-helix761-7633
α-helix765-7728
β-strand777-779318
α-helix780-7823
β-strand795-800618
β-strand803-804219
β-strand809-810219
β-strand813-819718
α-helix821-8299
β-strand851-857720
β-strand861121
β-strand862-864320
α-helix870-8723
β-strand877121
α-helix878-8803
α-helix883-8919
β-strand896-9071222
β-strand910-911217
β-strand975-9851122
β-strand992-998720
β-strand1003-1010820
α-helix10111
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-1Fprotein1106Oryctolagus cuniculusP13806 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8E56_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
>8E56_2 Voltage-dependent calcium channel gamma-1 subunit (chains E)
MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSPHMENHNTTCEAAHFGLWRICTKR
IALGEDRSCGPITLPGEKNCSYFRHFNPGESSEIFEFTTQKEYSISAAAISVFSLGFLIM
GTICALMAFRKKRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIDSEDTVWIEYYYSW
SFACACAAFVLLFLGGISLLLFSLPRMPQNPWESCMDAEPEH
Sequence of entity 3 (F), FASTA
>8E56_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
3PE1,2-Distearoyl-sn-glycerophosphoethanolamineC41 H82 N O8 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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