8E5A: PDB entry 8E5A

Human L-type voltage-gated calcium channel Cav1.3 treated with 1.4 mM Sofosbuvir at 3.3 Angstrom resolution. Determined by electron microscopy at 3.3 Å resolution. Released 7 Dec 2022.

Method
Electron microscopy
Resolution
3.3 Å
Organism
Homo sapiens
Chains
3
Atoms
20,257
Mol. weight
427.97 kDa
Ligands
CA, NAG
Released
7 Dec 2022

Explore 8E5A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E5A contains 119 α-helices and 79 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, 11 β-strands

ElementResiduesLengthSheet
α-helix129-14214
α-helix150-1523
α-helix156-17419
α-helix196-21621
α-helix236-24510
α-helix246-2538
α-helix255-26511
α-helix269-2713
α-helix272-29221
β-strand301-30331
β-strand30911
β-strand331-33331
α-helix350-36112
α-helix366-37611
α-helix382-3898
α-helix390-3967
α-helix397-41721
α-helix421-44020
α-helix517-5193
α-helix523-54018
α-helix549-57224
α-helix579-5824
α-helix586-60621
α-helix612-62211
α-helix624-6296
α-helix637-6459
α-helix647-67125
α-helix691-70313
α-helix707-71610
α-helix725-7295
α-helix730-74617
α-helix755-76713
α-helix878-8836
α-helix888-90316
α-helix914-93926
α-helix954-96916
α-helix980-9867
α-helix987-9948
α-helix999-101416
α-helix1017-103620
β-strand104312
β-strand1058-106253
α-helix1063-10653
β-strand1070-107453
β-strand107812
α-helix1087-109812
α-helix1103-11119
α-helix1126-11283
α-helix1129-11357
α-helix1136-11438
α-helix1144-115815
α-helix1172-11754
α-helix1177-11804
α-helix1193-120210
α-helix1205-122218
α-helix1231-125626
α-helix1261-12644
α-helix1268-128316
α-helix1284-12863
α-helix1320-13223
α-helix1337-134711
α-helix1351-137222
β-strand137514
α-helix1392-140312
α-helix1408-14147
β-strand142114
α-helix1440-146425
α-helix1467-14704
α-helix1479-148911
β-strand1499-150025
α-helix1505-15106
α-helix1527-15337
β-strand1544-154525
α-helix1546-155712
α-helix1566-157510
α-helix1585-15884
Chain C: 12 helices, 12 β-strands
ElementResiduesLengthSheet
α-helix39-5517
β-strand62-65422
β-strand71123
β-strand86123
β-strand92-98722
β-strand103-108622
β-strand115-119522
α-helix121-13111
α-helix156-1583
β-strand172122
α-helix178-1792
β-strand180-183424
α-helix191-20717
β-strand212-215424
α-helix247-26216
β-strand266-269424
α-helix277-2804
β-strand288-292524
α-helix297-3059
α-helix309-3135
α-helix315-32713
α-helix330-3323
β-strand335-337324
α-helix342-35918
Chain D: 42 helices, 56 β-strands
ElementResiduesLengthSheet
α-helix30-5122
α-helix54-629
β-strand68-7256
α-helix75-10935
β-strand122-12327
β-strand125-12628
β-strand142-14327
β-strand150-15129
β-strand158-15929
β-strand160110
β-strand165-16738
α-helix177-1859
α-helix189-19911
β-strand206-21058
β-strand215-21848
β-strand220110
α-helix238-2403
α-helix242-2487
β-strand252-259811
α-helix262-2643
α-helix267-28014
β-strand288111
β-strand289112
β-strand291-294411
β-strand298-300311
β-strand308112
α-helix312-32211
α-helix333-34311
β-strand355-362811
α-helix370-3767
β-strand383-389711
α-helix397-4059
β-strand410-413411
α-helix416-4183
α-helix419-4224
α-helix426-4305
α-helix432-4376
α-helix439-4413
β-strand445-44628
β-strand450-45128
β-strand458-467108
β-strand484-493108
α-helix494-4996
β-strand511-515513
β-strand520114
β-strand521-523313
α-helix531-5333
β-strand538115
β-strand560114
α-helix561-5644
α-helix569-57911
β-strand584-5931013
β-strand599116
β-strand600-6111213
β-strand618-624713
β-strand629-63356
α-helix639-6457
α-helix646-6483
α-helix650-6523
α-helix653-6564
β-strand658-659217
α-helix678-68811
α-helix700-71516
α-helix716-7205
β-strand726117
β-strand729-736817
β-strand741-743317
α-helix746-7516
α-helix758-7603
α-helix762-7698
β-strand773118
β-strand774-776317
α-helix777-7793
β-strand792-797617
β-strand800-801219
β-strand806-807219
β-strand810-816717
α-helix818-8269
β-strand848-854720
β-strand858121
β-strand859-861320
α-helix866-8694
β-strand874121
α-helix875-8773
α-helix880-8889
β-strand892-9041316
β-strand907115
β-strand972-9831216
β-strand989-994620
β-strand1001-1007720
α-helix10081
β-strand1011118
β-strand1013-1019720
α-helix1029-10324
β-strand1036-1038316
α-helix10401
α-helix10421
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
>8E5A_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
>8E5A_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
>8E5A_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
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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