8E5B: PDB entry 8E5B

Human L-type voltage-gated calcium channel Cav1.3 in the presence of Amiodarone and 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
20,310
Mol. weight
428.93 kDa
Ligands
BBI, WG6, CA, NAG
Released
7 Dec 2022

Explore 8E5B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E5B contains 120 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: 67 helices, 11 β-strands

ElementResiduesLengthSheet
α-helix128-14518
α-helix156-17823
α-helix196-21621
α-helix237-2459
α-helix247-2537
α-helix255-26612
α-helix269-2713
α-helix272-29221
β-strand301-30221
β-strand30911
β-strand332-33321
α-helix350-36112
α-helix366-37611
α-helix382-3909
α-helix391-3955
α-helix396-41924
α-helix421-43010
α-helix432-4409
α-helix517-5204
α-helix524-54017
α-helix549-57426
α-helix589-60618
α-helix615-6239
α-helix624-6296
α-helix636-64510
α-helix647-67226
α-helix691-70313
α-helix707-71610
α-helix725-7284
α-helix729-76840
α-helix878-8836
α-helix886-90318
α-helix914-93926
α-helix954-96916
α-helix980-9867
α-helix987-9893
α-helix991-9944
α-helix999-101416
α-helix1016-103621
β-strand1043-104422
β-strand1058-106253
α-helix1063-10653
β-strand1070-107453
β-strand1077-107822
α-helix1087-109812
α-helix1103-11119
α-helix1126-11283
α-helix1129-11357
α-helix1136-11438
α-helix1145-115915
α-helix1170-118011
α-helix1193-120210
α-helix1205-122218
α-helix1231-125828
α-helix1261-12644
α-helix1268-128114
α-helix1285-12873
α-helix1315-13195
α-helix1320-133213
α-helix1336-134914
α-helix1351-137222
β-strand137514
α-helix1376-13772
β-strand138415
β-strand138715
α-helix1392-140413
α-helix1408-14147
α-helix14201
β-strand142114
α-helix14221
α-helix1427-14282
α-helix1439-146527
α-helix1469-14713
α-helix1479-149214
α-helix1505-15117
α-helix1527-15337
α-helix1546-155712
α-helix1567-15759
Chain C: 12 helices, 11 β-strands
ElementResiduesLengthSheet
α-helix39-5416
α-helix55-573
β-strand63-65324
β-strand92-93224
β-strand94-95225
β-strand103-107525
β-strand115-119525
α-helix121-13313
α-helix156-1583
β-strand172-174324
β-strand180-183426
α-helix191-20717
β-strand212-215426
α-helix241-2444
α-helix247-26216
β-strand266-269426
α-helix278-2814
β-strand288-292526
α-helix297-3059
α-helix309-32618
α-helix330-3323
β-strand335-337326
α-helix342-35918
Chain D: 41 helices, 58 β-strands
ElementResiduesLengthSheet
α-helix30-5122
α-helix54-6411
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-helix186-1883
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-helix397-4048
β-strand410-413411
α-helix416-4183
α-helix419-4224
α-helix427-4304
α-helix432-4376
α-helix438-4414
β-strand445-446213
β-strand450-451214
β-strand458-461414
β-strand462-463213
β-strand464-46748
β-strand484-49078
β-strand491-493314
α-helix494-4996
β-strand511-515515
β-strand520116
β-strand521-523315
α-helix531-5333
β-strand538117
β-strand560116
α-helix561-5644
α-helix569-57911
β-strand584-5931015
β-strand599118
β-strand600-6111215
β-strand618-624715
β-strand629-63356
α-helix639-6468
α-helix650-6523
α-helix653-6564
β-strand658-661419
α-helix679-6879
α-helix700-71516
α-helix716-7205
β-strand729-736819
β-strand740-743419
α-helix746-7516
α-helix758-7603
α-helix762-7698
β-strand773120
β-strand774-776319
α-helix777-7793
β-strand792-797619
β-strand800-801221
β-strand806-807221
β-strand810-816719
α-helix818-8269
β-strand848-853622
β-strand858123
β-strand859-862422
β-strand874123
α-helix875-8773
α-helix880-8889
β-strand892-9041318
β-strand907117
β-strand972-9831218
β-strand990-994522
β-strand1001-1007722
α-helix10081
β-strand1011120
β-strand1014-1019622
β-strand1036-1037218
α-helix10401
α-helix10421
α-helix1043-10464
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
>8E5B_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
>8E5B_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
>8E5B_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
WG6SofosbuvirC22 H29 F N3 O9 P1
CACalcium ionCa2
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O61

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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