7UHF: PDB entry 7UHF

Human L-type voltage-gated calcium channel Cav1.3 in the presence of cinnarizine at 3.1 Angstrom resolution. Determined by electron microscopy at 3.1 Å resolution. Released 11 May 2022.

Method
Electron microscopy
Resolution
3.1 Å
Organism
Homo sapiens
Chains
3
Atoms
20,379
Mol. weight
429.8 kDa
Ligands
N90, CA, Y01, 3PE
Released
11 May 2022

Explore 7UHF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UHF contains 116 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-helix127-14418
α-helix156-17722
α-helix198-21619
α-helix238-24811
α-helix249-2535
α-helix255-26612
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-helix422-4276
α-helix430-44415
α-helix518-5214
α-helix523-54119
α-helix549-5568
α-helix558-57720
α-helix586-60419
α-helix612-62110
α-helix622-6265
α-helix627-6315
α-helix636-64611
α-helix647-6493
α-helix651-67222
α-helix691-70313
α-helix707-71610
α-helix723-7286
α-helix731-74717
α-helix749-7557
α-helix757-7604
α-helix763-7675
α-helix880-8845
α-helix888-90417
α-helix914-93926
α-helix957-96913
α-helix980-9867
α-helix994-9974
α-helix999-101214
α-helix1013-10153
α-helix1018-103619
β-strand104312
β-strand1058-106253
α-helix1063-10653
β-strand1070-107453
β-strand107812
α-helix1087-109812
α-helix1103-11119
α-helix1126-11283
α-helix1129-114315
α-helix1148-11514
α-helix1158-11603
α-helix1172-11809
α-helix1193-120210
α-helix1205-122218
α-helix1231-125929
α-helix1268-128215
α-helix1316-13205
α-helix1323-13253
α-helix1327-13304
α-helix1336-134914
α-helix1352-137221
β-strand137514
α-helix1392-140312
α-helix1408-14125
β-strand142114
α-helix1440-145314
α-helix1479-149113
β-strand1499-150025
α-helix1505-15106
α-helix1523-153311
β-strand1544-154525
α-helix1547-155711
α-helix1566-157510
α-helix1584-15874
Chain C: 11 helices, 12 β-strands
ElementResiduesLengthSheet
α-helix39-5416
β-strand62-66524
β-strand70-71225
β-strand86-87225
β-strand91-95524
β-strand103-108624
β-strand115-119524
α-helix121-13111
α-helix156-1583
β-strand171-172224
α-helix178-1792
β-strand180-183426
α-helix191-20717
β-strand212-215426
α-helix247-26115
β-strand266-269426
α-helix277-2804
β-strand288-292526
α-helix297-30711
α-helix315-32612
α-helix330-3323
β-strand335-337326
α-helix342-36019
Chain D: 38 helices, 57 β-strands
ElementResiduesLengthSheet
α-helix30-5223
α-helix54-6411
β-strand68-7256
α-helix75-10935
β-strand122-12437
β-strand125-12628
β-strand142-14437
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-helix333-34412
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-helix438-4414
β-strand445-446213
β-strand450-451214
β-strand458-461414
β-strand462-463213
β-strand464-46748
β-strand484-49078
β-strand491-493314
α-helix494-4985
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-strand600-6121315
β-strand617-624815
β-strand629-63356
α-helix638-6469
α-helix650-6523
α-helix653-6564
β-strand658-661418
α-helix679-68810
α-helix700-71516
α-helix716-7205
β-strand729-736818
β-strand740-743418
α-helix748-7503
α-helix758-7603
α-helix762-7698
β-strand773119
β-strand774-776318
β-strand792-797618
β-strand800-801220
β-strand806-807220
β-strand810-816718
α-helix818-8269
β-strand849-854621
β-strand858122
β-strand859-861321
α-helix866-8694
β-strand874122
α-helix875-8773
α-helix880-8889
β-strand892-9041323
β-strand907117
β-strand972-9831223
β-strand989-995721
β-strand1000-1007821
β-strand1011119
β-strand1013-1018621
β-strand1036-1038323
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
>7UHF_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
>7UHF_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
>7UHF_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
N901-(diphenylmethyl)-4-[(2E)-3-phenylprop-2-en-1-yl]piperazineC26 H28 N21
CACalcium ionCa2
Y01Cholesterol hemisuccinateC31 H50 O41
3PE1,2-Distearoyl-sn-glycerophosphoethanolamineC41 H82 N O8 P1
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O63

Primary citation

Structural basis for pore blockade of human voltage-gated calcium channel Ca v 1.3 by motion sickness drug cinnarizine. Yao, X., Gao, S., Yan, N. Cell Res (2022) 32:946-948. DOI 10.1038/s41422-022-00663-5 · 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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