8E59: PDB entry 8E59

Human L-type voltage-gated calcium channel Cav1.3 in the presence of Amiodarone at 3.1 Angstrom resolution. Determined by electron microscopy at 3.1 Å resolution. Released 7 Dec 2022.

Method
Electron microscopy
Resolution
3.1 Å
Organism
Homo sapiens
Chains
3
Atoms
20,309
Mol. weight
429.37 kDa
Ligands
BBI, 3PE, CA, NAG
Released
7 Dec 2022

Explore 8E59 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E59 contains 118 α-helices and 80 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: 65 helices, 12 β-strands

ElementResiduesLengthSheet
α-helix127-14418
α-helix156-18025
α-helix196-21722
α-helix238-2458
α-helix250-2534
α-helix255-26612
α-helix269-2713
α-helix272-29221
β-strand300-30341
β-strand30911
β-strand31611
β-strand331-33441
α-helix350-36112
α-helix366-37611
α-helix382-3909
α-helix391-3966
α-helix397-41923
α-helix421-43010
α-helix433-44412
α-helix523-54018
α-helix549-57426
α-helix580-5845
α-helix586-60621
α-helix614-6229
α-helix623-6264
α-helix627-6304
α-helix637-6459
α-helix647-67226
α-helix691-70313
α-helix707-71610
α-helix723-7297
α-helix730-77142
α-helix878-8836
α-helix888-90316
α-helix914-94128
α-helix954-96815
α-helix980-9867
α-helix987-9893
α-helix991-9944
α-helix999-103638
β-strand104312
β-strand1058-106253
α-helix1063-10653
β-strand1070-107453
β-strand107812
α-helix1087-109812
α-helix1103-11119
α-helix1126-11283
α-helix1129-11368
α-helix1137-11437
α-helix1144-115815
α-helix1170-11734
α-helix1176-11805
α-helix1193-120210
α-helix1205-122218
α-helix1231-125929
α-helix1264-12663
α-helix1268-128619
α-helix1315-13217
α-helix1322-13243
α-helix1325-13306
α-helix1336-134914
α-helix1353-137220
β-strand137514
α-helix1392-140413
α-helix1408-14147
β-strand142114
α-helix1439-146527
α-helix1467-14704
α-helix1479-149113
β-strand1499-150025
α-helix1505-15106
α-helix1527-15337
β-strand1544-154525
α-helix1546-155712
α-helix1567-15759
α-helix1584-15885
Chain C: 13 helices, 12 β-strands
ElementResiduesLengthSheet
α-helix39-5416
α-helix55-573
β-strand62-65423
β-strand70-71224
β-strand86-87224
β-strand92-98723
β-strand103-108623
β-strand115-119523
α-helix121-13111
α-helix156-1583
β-strand172123
β-strand180-183425
α-helix191-20717
β-strand212-215425
α-helix236-2383
α-helix247-26216
β-strand266-269425
α-helix277-2804
β-strand288-292525
α-helix297-3059
α-helix312-3143
α-helix315-32612
α-helix330-3323
β-strand335-337325
α-helix342-35918
Chain D: 40 helices, 56 β-strands
ElementResiduesLengthSheet
α-helix30-5223
α-helix54-6411
β-strand68-7256
α-helix75-10935
α-helix1211
β-strand122-12327
β-strand125-12628
β-strand142-14327
β-strand150-15129
β-strand158-15929
β-strand160110
β-strand165-16738
α-helix1731
α-helix177-1859
α-helix186-1883
α-helix189-19911
β-strand206-21058
β-strand215-21848
β-strand220110
α-helix238-2403
α-helix242-2487
β-strand252111
β-strand255-259512
α-helix262-2643
α-helix267-28014
β-strand289113
β-strand290-294512
β-strand298-300312
β-strand308113
α-helix312-32211
α-helix333-34311
β-strand355111
β-strand357-362612
α-helix370-3767
β-strand383-389712
α-helix397-4048
β-strand410-413412
α-helix416-4183
α-helix419-4224
α-helix426-4305
α-helix432-4376
α-helix438-4414
β-strand445-44628
β-strand450-45128
β-strand458-467108
β-strand484-493108
α-helix494-4996
β-strand511-515514
β-strand520115
β-strand521-523314
α-helix531-5333
β-strand538116
β-strand560115
α-helix561-5644
α-helix569-58012
β-strand584-5931014
β-strand599117
β-strand600-6111214
β-strand618-624714
β-strand629-63356
α-helix638-6469
α-helix650-6534
β-strand658-661418
α-helix678-68710
α-helix699-71517
α-helix716-7205
β-strand729-736818
β-strand740-743418
α-helix748-7514
α-helix758-7603
α-helix762-7698
β-strand773119
β-strand774-776318
α-helix777-7793
β-strand792-797618
β-strand800-801220
β-strand806-807220
β-strand810-816718
α-helix818-8269
β-strand848-854721
β-strand858122
β-strand859-861321
α-helix866-8694
β-strand874122
α-helix875-8773
α-helix880-8889
β-strand892-9041317
β-strand907116
β-strand972-9831217
β-strand989-994621
β-strand1001-1007721
β-strand1011119
β-strand1013-1019721
α-helix1029-10313
β-strand1036-1038317
α-helix1050-10523

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Voltage-dependent L-type calcium channel subunit alpha-1DAprotein2161Homo sapiensQ01668 (AlphaFold model)
Voltage-dependent calcium channel subunit alpha-2/delta-1Dprotein1103Homo sapiensP54289 (AlphaFold model)
Voltage-dependent L-type calcium channel subunit beta-3Cprotein484Homo sapiensP54284 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8E59_1 Voltage-dependent L-type calcium channel subunit alpha-1D (chains A)
MMMMMMMKKMQHQRQQQADHANEANYARGTRLPLSGEGPTSQPNSSKQTVLSWQAAIDAA
RQAKAAQTMSTSAPPPVGSLSQRKRQQYAKSKKQGNSSNSRPARALFCLSLNNPIRRACI
SIVEWKPFDIFILLAIFANCVALAIYIPFPEDDSNSTNHNLEKVEYAFLIIFTVETFLKI
IAYGLLLHPNAYVRNGWNLLDFVIVIVGLFSVILEQLTKETEGGNHSSGKSGGFDVKALR
AFRVLRPLRLVSGVPSLQVVLNSIIKAMVPLLHIALLVLFVIIIYAIIGLELFIGKMHKT
CFFADSDIVAEEDPAPCAFSGNGRQCTANGTECRSGWVGPNGGITNFDNFAFAMLTVFQC
ITMEGWTDVLYWMNDAMGFELPWVYFVSLVIFGSFFVLNLVLGVLSGEFSKEREKAKARG
DFQKLREKQQLEEDLKGYLDWITQAEDIDPENEEEGGEEGKRNTSMPTSETESVNTENVS
GEGENRGCCGSLCQAISKSKLSRRWRRWNRFNRRRCRAAVKSVTFYWLVIVLVFLNTLTI
SSEHYNQPDWLTQIQDIANKVLLALFTCEMLVKMYSLGLQAYFVSLFNRFDCFVVCGGIT
ETILVELEIMSPLGISVFRCVRLLRIFKVTRHWTSLSNLVASLLNSMKSIASLLLLLFLF
IIIFSLLGMQLFGGKFNFDETQTKRSTFDNFPQALLTVFQILTGEDWNAVMYDGIMAYGG
PSSSGMIVCIYFIILFICGNYILLNVFLAIAVDNLADAESLNTAQKEEAEEKERKKIARK
ESLENKKNNKPEVNQIANSDNKVTIDDYREEDEDKDPYPPCDVPVGEEEEEEEEDEPEVP
AGPRPRRISELNMKEKIAPIPEGSAFFILSKTNPIRVGCHKLINHHIFTNLILVFIMLSS
AALAAEDPIRSHSFRNTILGYFDYAFTAIFTVEILLKMTTFGAFLHKGAFCRNYFNLLDM
LVVGVSLVSFGIQSSAISVVKILRVLRVLRPLRAINRAKGLKHVVQCVFVAIRTIGNIMI
VTTLLQFMFACIGVQLFKGKFYRCTDEAKSNPEECRGLFILYKDGDVDSPVVRERIWQNS
DFNFDNVLSAMMALFTVSTFEGWPALLYKAIDSNGENIGPIYNHRVEISIFFIIYIIIVA
FFMMNIFVGFVIVTFQEQGEKEYKNCELDKNQRQCVEYALKARPLRRYIPKNPYQYKFWY
VVNSSPFEYMMFVLIMLNTLCLAMQHYEQSKMFNDAMDILNMVFTGVFTVEMVLKVIAFK
PKGYFSDAWNTFDSLIVIGSIIDVALSEADPTESENVPVPTATPGNSEESNRISITFFRL
FRVMRLVKLLSRGEGIRTLLWTFIKSFQALPYVALLIAMLFFIYAVIGMQMFGKVAMRDN
NQINRNNNFQTFPQAVLLLFRCATGEAWQEIMLACLPGKLCDPESDYNPGEEYTCGSNFA
IVYFISFYMLCAFLIINLFVAVIMDNFDYLTRDWSILGPHHLDEFKRIWSEYDPEAKGRI
KHLDVVTLLRRIQPPLGFGKLCPHRVACKRLVAMNMPLNSDGTVMFNATLFALVRTALKI
KTEGNLEQANEELRAVIKKIWKKTSMKLLDQVVPPAGDDEVTVGKFYATFLIQDYFRKFK
KRKEQGLVGKYPAKNTTIALQAGLRTLHDIGPEIRRAISCDLQDDEPEETKREEEDDVFK
RNGALLGNHVNHVNSDRRDSLQQTNTTHRPLHVQRPSIPPASDTEKPLFPPAGNSVCHNH
HNHNSIGKQVPTSTNANLNNANMSKAAHGKRPSIGNLEHVSENGHHSSHKHDREPQRRSS
VKRTRYYETYIRSDSGDEQLPTICREDPEIHGYFRDPHCLGEQEYFSSEECYEDDSSPTW
SRQNYGYYSRYPGRNIDSERPRGYHHPQGFLEDDDSPVCYDSRRSPRRRLLPPTPASHRR
SSFNFECLRRQSSQEEVPSSPIFPHRTALPLHLMQQQIMAVAGLDSSKAQKYSPSHSTRS
WATPPATPPYRDWTPCYTPLIQVEQSEALDQVNGSLPSLHRSSWYTDEPDISYRTFTPAS
LTVPSSFRNKNSDKQRSADSLVEAVLISEGLGRYARDPKFVSATKHEIADACDLTIDEME
SAASTLLNGNVRPRANGDVGPLSHRQDYELQDFGPGYSDEEPDPGRDEEDLADEMICITT
L
Sequence of entity 2 (D), FASTA
>8E59_2 Voltage-dependent calcium channel subunit alpha-2/delta-1 (chains D)
MAAGCLLALTLTLFQSLLIGPSSEEPFPSAVTIKSWVDKMQEDLVTLAKTASGVNQLVDI
YEKYQDLYTVEPNNARQLVEIAARDIEKLLSNRSKALVRLALEAEKVQAAHQWREDFASN
EVVYYNAKDDLDPEKNDSEPGSQRIKPVFIEDANFGRQISYQHAAVHIPTDIYEGSTIVL
NELNWTSALDEVFKKNREEDPSLLWQVFGSATGLARYYPASPWVDNSRTPNKIDLYDVRR
RPWYIQGAASPKDMLILVDVSGSVSGLTLKLIRTSVSEMLETLSDDDFVNVASFNSNAQD
VSCFQHLVQANVRNKKVLKDAVNNITAKGITDYKKGFSFAFEQLLNYNVSRANCNKIIML
FTDGGEERAQEIFNKYNKDKKVRVFTFSVGQHNYDRGPIQWMACENKGYYYEIPSIGAIR
INTQEYLDVLGRPMVLAGDKAKQVQWTNVYLDALELGLVITGTLPVFNITGQFENKTNLK
NQLILGVMGVDVSLEDIKRLTPRFTLCPNGYYFAIDPNGYVLLHPNLQPKPIGVGIPTIN
LRKRRPNIQNPKSQEPVTLDFLDAELENDIKVEIRNKMIDGESGEKTFRTLVKSQDERYI
DKGNRTYTWTPVNGTDYSLALVLPTYSFYYIKAKLEETITQARYSETLKPDNFEESGYTF
IAPRDYCNDLKISDNNTEFLLNFNEFIDRKTPNNPSCNADLINRVLLDAGFTNELVQNYW
SKQKNIKGVKARFVVTDGGITRVYPKEAGENWQENPETYEDSFYKRSLDNDNYVFTAPYF
NKSGPGAYESGIMVSKAVEIYIQGKLLKPAVVGIKIDVNSWIENFTKTSIRDPCAGPVCD
CKRNSDVMDCVILDDGGFLLMANHDDYTNQIGRFFGEIDPSLMRHLVNISVYAFNKSYDY
QSVCEPGAAPKQGAGHRSAYVPSVADILQIGWWATAAAWSILQQFLLSLTFPRLLEAVEM
EDDDFTASLSKQSCITEQTQYFFDNDSKSFSGVLDCGNCSRIFHGEKLMNTNLIFIMVES
KGTCPCDTRLLIQAEQTSDGPNPCDMVKQPRYRKGPDVCFDNNVLEDYTDCGGVSGLNPS
LWYIIGIQFLLLWLVSGSTHRLL
Sequence of entity 3 (C), FASTA
>8E59_3 Voltage-dependent L-type calcium channel subunit beta-3 (chains C)
MYDDSYVPGFEDSEAGSADSYTSRPSLDSDVSLEEDRESARREVESQAQQQLERAKHKPV
AFAVRTNVSYCGVLDEECPVQGSGVNFEAKDFLHIKEKYSNDWWIGRLVKEGGDIAFIPS
PQRLESIRLKQEQKARRSGNPSSLSDIGNRRSPPPSLAKQKQKQAEHVPPYDVVPSMRPV
VLVGPSLKGYEVTDMMQKALFDFLKHRFDGRISITRVTADLSLAKRSVLNNPGKRTIIER
SSARSSIAEVQSEIERIFELAKSLQLVVLDADTINHPAQLAKTSLAPIIVFVKVSSPKVL
QRLIRSRGKSQMKHLTVQMMAYDKLVQCPPESFDVILDENQLEDACEHLAEYLEVYWRAT
HHPAPGPGLLGPPSAIPGLQNQQLLGERGEEHSPLERDSLMPSDEASESSRQAWTGSSQR
SSRHLEEDYADAYQDLYQPHRQHTSGLPSANGHDPQDRLLAQDSEHNHSDRNWQRNRPWP
KDSY

Ligands and cofactors

IDNameFormulaCopies
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
CACalcium ionCa2
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O62

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 Q01668 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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