7VFS: PDB entry 7VFS

Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, apo state. Determined by electron microscopy at 2.8 Å resolution. Released 3 Nov 2021.

Method
Electron microscopy
Resolution
2.8 Å
Organism
Homo sapiens
Chains
3
Atoms
19,764
Mol. weight
463.52 kDa
Ligands
R16, Y01, PT5, CA
Released
3 Nov 2021

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

Secondary structure: helices and β-sheets

7VFS contains 122 α-helices and 77 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: 72 helices, 17 β-strands

ElementResiduesLengthSheet
α-helix95-11420
α-helix125-1328
α-helix134-15017
α-helix165-17915
α-helix186-1916
α-helix194-1974
α-helix201-2055
α-helix207-21711
α-helix223-24523
β-strand252-25431
α-helix261-2622
β-strand26711
α-helix275-2773
β-strand282-28431
α-helix291-2933
α-helix300-31112
α-helix316-32611
α-helix333-3408
α-helix341-3466
α-helix347-36317
α-helix366-40540
α-helix463-47917
α-helix482-50019
α-helix508-53629
α-helix538-5414
α-helix545-56622
α-helix575-58814
α-helix592-60413
α-helix606-63126
β-strand63712
β-strand64012
α-helix649-66113
α-helix665-67410
β-strand67513
β-strand67713
α-helix683-6853
α-helix686-6949
α-helix697-74145
β-strand76614
α-helix767-78115
α-helix1141-11477
α-helix1152-116817
α-helix1178-120528
α-helix1218-123518
α-helix1245-12528
α-helix1253-12608
α-helix1261-12644
α-helix1266-128116
α-helix1283-130422
β-strand1309-131135
β-strand1325-132846
β-strand1335-133846
β-strand1341-134335
α-helix1351-136313
α-helix1367-13759
α-helix1390-13923
α-helix1393-14008
α-helix1401-14077
α-helix1408-141710
β-strand142014
α-helix1435-14439
α-helix1460-146910
α-helix1471-148919
α-helix1499-152426
α-helix1527-15315
α-helix1536-155520
α-helix1556-15583
α-helix1562-15643
α-helix1566-15683
α-helix1569-15735
α-helix1574-15763
α-helix1577-15815
α-helix1583-159715
α-helix1602-162120
β-strand162417
α-helix1625-16262
α-helix1641-165212
α-helix1657-16637
β-strand1668-166928
β-strand167017
α-helix16711
β-strand1678-167928
α-helix1683-170927
α-helix1711-17144
α-helix1723-17319
α-helix1748-17547
α-helix1793-180210
α-helix1813-182715
α-helix1837-18448
Chain B: 40 helices, 55 β-strands
ElementResiduesLengthSheet
α-helix30-4819
α-helix49-535
α-helix54-6310
β-strand68-7259
α-helix75-10935
β-strand122-124310
β-strand125-126211
β-strand142-144310
α-helix1451
β-strand150-152312
β-strand157-159312
β-strand160113
β-strand165-167311
α-helix177-1859
α-helix187-19812
β-strand206-210511
β-strand215-217311
β-strand220113
β-strand229114
β-strand232114
α-helix238-2403
α-helix242-2476
α-helix250-2523
β-strand253-258615
α-helix262-2643
α-helix267-28014
β-strand288-294715
β-strand298-300315
β-strand308-309215
α-helix312-32312
α-helix333-34412
β-strand356-362715
α-helix370-3767
β-strand382-389815
α-helix397-4048
β-strand409-413515
α-helix419-43012
α-helix432-4365
β-strand445-446211
α-helix447-4493
β-strand450-451211
β-strand458-4671011
β-strand484-4931011
α-helix494-4985
β-strand511-515516
β-strand520117
β-strand523116
α-helix531-5333
β-strand560117
α-helix561-5644
α-helix570-57910
β-strand584-5931016
β-strand600-6111216
β-strand618-624716
β-strand629-63359
α-helix640-6467
β-strand658118
β-strand667119
α-helix670-6723
α-helix676-68813
β-strand697119
α-helix699-71517
α-helix716-7205
β-strand729-736818
β-strand743118
α-helix758-7603
α-helix762-7698
β-strand773120
β-strand774-776318
α-helix777-7793
β-strand792-797618
β-strand801-802221
β-strand805-806221
β-strand810-816718
α-helix818-82710
α-helix828-8303
β-strand851-853322
α-helix855-8573
β-strand858123
β-strand859-862422
α-helix868-8703
β-strand874123
α-helix875-8784
α-helix880-88910
β-strand892-9041324
β-strand972-9831224
β-strand989-994622
β-strand1001-1007722
α-helix10081
β-strand1011120
β-strand1014-1016322
β-strand1019122
β-strand1036-1037224
α-helix1043-10464
α-helix1050-10523
Chain D: 10 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix2301
β-strand231-235525
α-helix243-25917
β-strand264-268525
α-helix273-2753
α-helix302-31312
β-strand318-322525
α-helix330-3323
β-strand340-344525
α-helix349-35810
α-helix363-3664
α-helix367-37913
α-helix382-3843
β-strand387-389325
α-helix394-41118

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Voltage-dependent N-type calcium channel subunit alpha-1BAprotein2339Homo sapiensQ00975 (AlphaFold model)
Voltage-dependent calcium channel subunit alpha-2/delta-1Bprotein1103Homo sapiensP54289 (AlphaFold model)
Voltage-dependent L-type calcium channel subunit beta-1Dprotein598Homo sapiensQ02641 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>7VFS_1 Voltage-dependent N-type calcium channel subunit alpha-1B (chains A)
MVRFGDELGGRYGGPGGGERARGGGAGGAGGPGPGGLQPGQRVLYKQSIAQRARTMALYN
PIPVKQNCFTVNRSLFVFSEDNVVRKYAKRITEWPPFEYMILATIIANCIVLALEQHLPD
GDKTPMSERLDDTEPYFIGIFCFEAGIKIIALGFVFHKGSYLRNGWNVMDFVVVLTGILA
TAGTDFDLRTLRAVRVLRPLKLVSGIPSLQVVLKSIMKAMVPLLQIGLLLFFAILMFAII
GLEFYMGKFHKACFPNSTDAEPVGDFPCGKEAPARLCEGDTECREYWPGPNFGITNFDNI
LFAILTVFQCITMEGWTDILYNTNDAAGNTWNWLYFIPLIIIGSFFMLNLVLGVLSGEFA
KERERVENRRAFLKLRRQQQIERELNGYLEWIFKAEEVMLAEEDRNAEEKSPLDVLKRAA
TKKSRNDLIHAEEGEDRFADLCAVGSPFARASLKSGKTESSSYFRRKEKMFRFFIRRMVK
AQSFYWVVLCVVALNTLCVAMVHYNQPRRLTTTLYFAEFVFLGLFLTEMSLKMYGLGPRS
YFRSSFNCFDFGVIVGSVFEVVWAAIKPGSSFGISVLRALRLLRIFKVTKYWSSLRNLVV
SLLNSMKSIISLLFLLFLFIVVFALLGMQLFGGQFNFQDETPTTNFDTFPAAILTVFQIL
TGEDWNAVMYHGIESQGGVSKGMFSSFYFIVLTLFGNYTLLNVFLAIAVDNLANAQELTK
DEEEMEEAANQKLALQKAKEVAEVSPMSAANISIAARQQNSAKARSVWEQRASQLRLQNL
RASCEALYSEMDPEERLRFATTRHLRPDMKTHLDRPLVVELGRDGARGPVGGKARPEAAE
APEGVDPPRRHHRHRDKDKTPAAGDQDRAEAPKAESGEPGAREERPRPHRSHSKEAAGPP
EARSERGRGPGPEGGRRHHRRGSPEEAAEREPRRHRAHRHQDPSKECAGAKGERRARHRG
GPRAGPREAESGEEPARRHRARHKAQPAHEAVEKETTEKEATEKEAEIVEADKEKELRNH
QPREPHCDLETSGTVTVGPMHTLPSTCLQKVEEQPEDADNQRNVTRMGSQPPDPNTIVHI
PVMLTGPLGEATVVPSGNVDLESQAEGKKEVEADDVMRSGPRPIVPYSSMFCLSPTNLLR
RFCHYIVTMRYFEVVILVVIALSSIALAAEDPVRTDSPRNNALKYLDYIFTGVFTFEMVI
KMIDLGLLLHPGAYFRDLWNILDFIVVSGALVAFAFSGSKGKDINTIKSLRVLRVLRPLK
TIKRLPKLKAVFDCVVNSLKNVLNILIVYMLFMFIFAVIAVQLFKGKFFYCTDESKELER
DCRGQYLDYEKEEVEAQPRQWKKYDFHYDNVLWALLTLFTVSTGEGWPMVLKHSVDATYE
EQGPSPGYRMELSIFYVVYFVVFPFFFVNIFVALIIITFQEQGDKVMSECSLEKNERACI
DFAISAKPLTRYMPQNRQSFQYKTWTFVVSPPFEYFIMAMIALNTVVLMMKFYDAPYEYE
LMLKCLNIVFTSMFSMECVLKIIAFGVLNYFRDAWNVFDFVTVLGSITDILVTEIAETNN
FINLSFLRLFRAARLIKLLRQGYTIRILLWTFVQSFKALPYVCLLIAMLFFIYAIIGMQV
FGNIALDDDTSINRHNNFRTFLQALMLLFRSATGEAWHEIMLSCLSNQACDEQANATECG
SDFAYFYFVSFIFLCSFLMLNLFVAVIMDNFEYLTRDSSILGPHHLDEFIRVWAEYDPAA
CGRISYNDMFEMLKHMSPPLGLGKKCPARVAYKRLVRMNMPISNEDMTVHFTSTLMALIR
TALEIKLAPAGTKQHQCDAELRKEISVVWANLPQKTLDLLVPPHKPDEMTVGKVYAALMI
FDFYKQNKTTRDQMQQAPGGLSQMGPVSLFHPLKATLEQTQPAVLRGARVFLRQKSSTSL
SNGGAIQNQESGIKESVSWGTQRTQDAPHEARPPLERGHSTEIPVGRSGALAVDVQMQSI
TRRGPDGEPQPGLESQGRAASMPRLAAETQPVTDASPMKRSISTLAQRPRGTHLCSTTPD
RPPPSQASSHHHHHRCHRRRDRKQRSLEKGPSLSADMDGAPSSAVGPGLPPGEGPTGCRR
ERERRQERGRSQERRQPSSSSSEKQRFYSCDRFGGREPPKPKPSLSSHPTSPTAGQEPGP
HPQGSGSVNGSPLLSTSGASTPGRGGRRQLPQTPLTPRPSITYKTANSSPIHFAGAQTSL
PAFSPGRLSRGLSEHNALLQRDPLSQPLAPGSRIGSDPYLGQRLDSEASVHALPEDTLTF
EEAVATNSGRSSRTSYVSSLTSQSHPLRRVPNGYHCTLGLSSGGRARHSYHHPDQDHWC
Sequence of entity 2 (B), FASTA
>7VFS_2 Voltage-dependent calcium channel subunit alpha-2/delta-1 (chains B)
MAAGCLLALTLTLFQSLLIGPSSEEPFPSAVTIKSWVDKMQEDLVTLAKTASGVNQLVDI
YEKYQDLYTVEPNNARQLVEIAARDIEKLLSNRSKALVRLALEAEKVQAAHQWREDFASN
EVVYYNAKDDLDPEKNDSEPGSQRIKPVFIEDANFGRQISYQHAAVHIPTDIYEGSTIVL
NELNWTSALDEVFKKNREEDPSLLWQVFGSATGLARYYPASPWVDNSRTPNKIDLYDVRR
RPWYIQGAASPKDMLILVDVSGSVSGLTLKLIRTSVSEMLETLSDDDFVNVASFNSNAQD
VSCFQHLVQANVRNKKVLKDAVNNITAKGITDYKKGFSFAFEQLLNYNVSRANCNKIIML
FTDGGEERAQEIFNKYNKDKKVRVFTFSVGQHNYDRGPIQWMACENKGYYYEIPSIGAIR
INTQEYLDVLGRPMVLAGDKAKQVQWTNVYLDALELGLVITGTLPVFNITGQFENKTNLK
NQLILGVMGVDVSLEDIKRLTPRFTLCPNGYYFAIDPNGYVLLHPNLQPKPIGVGIPTIN
LRKRRPNIQNPKSQEPVTLDFLDAELENDIKVEIRNKMIDGESGEKTFRTLVKSQDERYI
DKGNRTYTWTPVNGTDYSLALVLPTYSFYYIKAKLEETITQARYSETLKPDNFEESGYTF
IAPRDYCNDLKISDNNTEFLLNFNEFIDRKTPNNPSCNADLINRVLLDAGFTNELVQNYW
SKQKNIKGVKARFVVTDGGITRVYPKEAGENWQENPETYEDSFYKRSLDNDNYVFTAPYF
NKSGPGAYESGIMVSKAVEIYIQGKLLKPAVVGIKIDVNSWIENFTKTSIRDPCAGPVCD
CKRNSDVMDCVILDDGGFLLMANHDDYTNQIGRFFGEIDPSLMRHLVNISVYAFNKSYDY
QSVCEPGAAPKQGAGHRSAYVPSVADILQIGWWATAAAWSILQQFLLSLTFPRLLEAVEM
EDDDFTASLSKQSCITEQTQYFFDNDSKSFSGVLDCGNCSRIFHGEKLMNTNLIFIMVES
KGTCPCDTRLLIQAEQTSDGPNPCDMVKQPRYRKGPDVCFDNNVLEDYTDCGGVSGLNPS
LWYIIGIQFLLLWLVSGSTHRLL
Sequence of entity 3 (D), FASTA
>7VFS_3 Voltage-dependent L-type calcium channel subunit beta-1 (chains D)
MVQKTSMSRGPYPPSQEIPMEVFDPSPQGKYSKRKGRFKRSDGSTSSDTTSNSFVRQGSA
ESYTSRPSDSDVSLEEDREALRKEAERQALAQLEKAKTKPVAFAVRTNVGYNPSPGDEVP
VQGVAITFEPKDFLHIKEKYNNDWWIGRLVKEGCEVGFIPSPVKLDSLRLLQEQKLRQNR
LGSSKSGDNSSSSLGDVVTGTRRPTPPASAKQKQKSTEHVPPYDVVPSMRPIILVGPSLK
GYEVTDMMQKALFDFLKHRFDGRISITRVTADISLAKRSVLNNPSKHIIIERSNTRSSLA
EVQSEIERIFELARTLQLVALDADTINHPAQLSKTSLAPIIVYIKITSPKVLQRLIKSRG
KSQSKHLNVQIAASEKLAQCPPEMFDIILDENQLEDACEHLAEYLEAYWKATHPPSSTPP
NPLLNRTMATAALAASPAPVSNLQGPYLASGDQPLERATGEHASMHEYPGELGQPPGLYP
SSHPPGRAGTLRALSRQDTFDADTPGSRNSAYTELGDSCVDMETDPSEGPGLGDPAGGGT
PPARQGSWEDEEEDYEEELTDNRNRGRNKARYCAEGGGPVLGRNKNELEGWGRGVYIR

Ligands and cofactors

IDNameFormulaCopies
R16HexadecaneC16 H3418
Y01Cholesterol hemisuccinateC31 H50 O43
PT5[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4…C47 H85 O19 P31
CACalcium ionCa2
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O68

Primary citation

Closed-state inactivation and pore-blocker modulation mechanisms of human Ca V 2.2. Dong, Y., Gao, Y., Xu, S. et al. Cell Rep (2021) 37:109931-109931. DOI 10.1016/j.celrep.2021.109931 · PubMed

Other PDB entries of the same protein (UniProt Q00975 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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