7VFU: PDB entry 7VFU

Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, bound to ziconotide. Determined by electron microscopy at 3.0 Å resolution. Released 3 Nov 2021.

Method
Electron microscopy
Resolution
3.0 Å
Organisms
Homo sapiens, Conus magus
Chains
4
Atoms
19,946
Mol. weight
466.17 kDa
Ligands
R16, Y01, PT5, CA
Released
3 Nov 2021

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

Secondary structure: helices and β-sheets

7VFU contains 124 α-helices and 81 β-strands across 4 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: 73 helices, 14 β-strands

ElementResiduesLengthSheet
α-helix89-924
α-helix95-11319
α-helix125-1328
α-helix134-15118
β-strand15311
β-strand16011
α-helix165-17915
α-helix187-1915
α-helix195-1973
α-helix200-2056
α-helix207-21812
α-helix223-24523
β-strand25212
β-strand253-25423
α-helix261-2622
β-strand26712
α-helix275-2773
β-strand282-28323
α-helix291-2933
α-helix300-31112
α-helix316-32611
α-helix332-3409
α-helix341-3455
α-helix346-36318
α-helix366-40439
α-helix463-47816
α-helix484-50017
α-helix508-53629
α-helix538-5414
α-helix545-56622
α-helix575-58814
α-helix592-60413
α-helix606-63126
α-helix649-66012
α-helix665-67511
α-helix683-6853
α-helix687-69711
α-helix699-74042
α-helix767-78115
α-helix1141-11477
α-helix1152-116918
α-helix1178-120528
α-helix1218-123619
α-helix1245-12528
α-helix1253-12564
α-helix1258-12603
α-helix1261-12644
α-helix1266-128116
α-helix1283-130422
β-strand1309-131134
β-strand1325-132845
β-strand1335-133845
α-helix13391
β-strand1341-134334
α-helix1351-136212
α-helix1367-137610
α-helix1390-13934
α-helix1394-14007
α-helix1401-14077
α-helix1408-141710
α-helix1435-14439
α-helix1460-146910
α-helix1471-148919
α-helix1498-152427
α-helix1527-15304
α-helix1536-155520
α-helix1556-15583
α-helix1566-15683
α-helix1569-15735
α-helix1576-15816
α-helix1583-159715
α-helix1600-162122
β-strand162416
α-helix1641-165212
α-helix1657-16637
β-strand166817
α-helix16691
β-strand167016
α-helix16711
β-strand167917
α-helix1684-170825
α-helix1711-17144
α-helix1723-17319
α-helix1748-17547
α-helix1792-180211
α-helix1813-182715
α-helix1837-18448
Chain B: 42 helices, 59 β-strands
ElementResiduesLengthSheet
α-helix30-5223
α-helix54-6310
α-helix65-673
β-strand68-72510
α-helix75-10935
β-strand122-124311
β-strand125-126212
β-strand142-144311
α-helix1491
β-strand150-151213
β-strand158-159213
β-strand160114
β-strand165-166212
α-helix177-1859
α-helix187-19913
β-strand206-210512
β-strand216-217212
β-strand220114
β-strand229115
β-strand232115
α-helix238-2403
α-helix242-2476
β-strand253116
β-strand256-258317
α-helix262-2643
α-helix267-28014
β-strand288-289216
β-strand291-294417
β-strand298-300317
β-strand308-309216
α-helix312-32312
α-helix333-34311
β-strand356116
β-strand357-362617
α-helix370-3767
β-strand383-389717
α-helix397-4059
β-strand409-413517
α-helix419-43012
α-helix432-4365
β-strand445-446212
α-helix447-4493
β-strand450-451212
β-strand458-4671012
β-strand484-4931012
α-helix494-4974
α-helix498-5003
β-strand511-515518
β-strand520119
β-strand523118
α-helix531-5333
β-strand560119
α-helix561-5644
α-helix570-57910
β-strand584-588518
β-strand591-593320
β-strand600-602320
β-strand605-611718
β-strand618-622518
α-helix625-6284
β-strand629-633510
α-helix640-6456
β-strand658121
β-strand667122
α-helix671-6722
α-helix676-68813
β-strand697122
α-helix699-71517
α-helix716-7205
β-strand729-736821
β-strand743121
α-helix748-7514
α-helix758-7603
α-helix762-7698
β-strand774-776321
α-helix777-7793
β-strand792-797621
β-strand801-802223
β-strand805-806223
β-strand810-816721
α-helix818-82710
α-helix828-8303
β-strand851-853324
α-helix855-8573
β-strand858125
β-strand859-862424
α-helix868-8703
β-strand874125
α-helix875-8784
α-helix880-8889
β-strand892-896526
β-strand899-904627
β-strand972-977627
β-strand979-983526
β-strand989-994624
β-strand1001-1007724
α-helix10081
β-strand1014-1016324
β-strand1036-1038327
α-helix1043-10464
α-helix1050-10523
Chain D: 8 helices, 5 β-strands
ElementResiduesLengthSheet
β-strand232-23549
α-helix243-25917
β-strand264-26969
α-helix273-2753
α-helix302-31413
β-strand318-32369
α-helix329-3324
β-strand340-34459
α-helix349-35810
α-helix363-3653
α-helix368-37912
β-strand387-38939
α-helix394-41118
Chain E: 1 helix, 3 β-strands
ElementResiduesLengthSheet
β-strand718
α-helix10-123
β-strand2118
β-strand2418

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Voltage-dependent N-type calcium channel subunit alpha-1BAprotein2339Homo sapiensQ00975 (AlphaFold model)
Omega-conotoxin MVIIAEprotein25Conus magusP05484 (AlphaFold model)
Voltage-dependent L-type calcium channel subunit beta-1Dprotein598Homo sapiensQ02641 (AlphaFold model)
Voltage-dependent calcium channel subunit alpha-2/delta-1Bprotein1103Homo sapiensP54289 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>7VFU_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 (E), FASTA
>7VFU_2 Omega-conotoxin MVIIA (chains E)
CKGKGAKCSRLMYDCCTGSCRSGKC
Sequence of entity 3 (D), FASTA
>7VFU_3 Voltage-dependent L-type calcium channel subunit beta-1 (chains D)
MVQKTSMSRGPYPPSQEIPMEVFDPSPQGKYSKRKGRFKRSDGSTSSDTTSNSFVRQGSA
ESYTSRPSDSDVSLEEDREALRKEAERQALAQLEKAKTKPVAFAVRTNVGYNPSPGDEVP
VQGVAITFEPKDFLHIKEKYNNDWWIGRLVKEGCEVGFIPSPVKLDSLRLLQEQKLRQNR
LGSSKSGDNSSSSLGDVVTGTRRPTPPASAKQKQKSTEHVPPYDVVPSMRPIILVGPSLK
GYEVTDMMQKALFDFLKHRFDGRISITRVTADISLAKRSVLNNPSKHIIIERSNTRSSLA
EVQSEIERIFELARTLQLVALDADTINHPAQLSKTSLAPIIVYIKITSPKVLQRLIKSRG
KSQSKHLNVQIAASEKLAQCPPEMFDIILDENQLEDACEHLAEYLEAYWKATHPPSSTPP
NPLLNRTMATAALAASPAPVSNLQGPYLASGDQPLERATGEHASMHEYPGELGQPPGLYP
SSHPPGRAGTLRALSRQDTFDADTPGSRNSAYTELGDSCVDMETDPSEGPGLGDPAGGGT
PPARQGSWEDEEEDYEEELTDNRNRGRNKARYCAEGGGPVLGRNKNELEGWGRGVYIR
Sequence of entity 4 (B), FASTA
>7VFU_4 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

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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