7VFV: PDB entry 7VFV

Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, bound to PD173212. Determined by electron microscopy at 3.0 Å resolution. Released 3 Nov 2021.

Method
Electron microscopy
Resolution
3.0 Å
Organism
Homo sapiens
Chains
3
Atoms
19,776
Mol. weight
463.66 kDa
Ligands
6IX, CA, PT5, Y01
Released
3 Nov 2021

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

Secondary structure: helices and β-sheets

7VFV contains 124 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: 73 helices, 12 β-strands

ElementResiduesLengthSheet
α-helix95-11319
α-helix127-1326
α-helix134-15118
α-helix165-17915
α-helix187-1915
α-helix193-1975
α-helix200-2056
α-helix207-21812
α-helix223-24523
β-strand252-25431
α-helix261-2622
β-strand282-28431
α-helix290-2934
α-helix300-31112
α-helix316-32611
α-helix333-3408
α-helix341-3455
α-helix346-36318
α-helix366-40439
α-helix463-47816
α-helix482-50019
α-helix508-53629
α-helix538-5414
α-helix545-56622
α-helix575-58814
α-helix592-60413
α-helix607-63125
α-helix649-66113
α-helix665-67511
α-helix679-6824
α-helix683-6853
α-helix687-6948
α-helix699-74042
β-strand76612
α-helix767-78115
α-helix1141-11477
α-helix1152-116817
α-helix1178-120528
α-helix1218-123518
α-helix1245-12528
α-helix1253-12564
α-helix1258-12603
α-helix1261-12644
α-helix1266-128116
α-helix1283-130422
β-strand1309-131133
β-strand1325-132844
β-strand1335-133844
β-strand1341-134333
α-helix1351-136212
α-helix1367-13759
α-helix1390-13934
α-helix1394-14007
α-helix1401-14077
α-helix1408-141710
β-strand142012
α-helix1435-14439
α-helix1460-146910
α-helix1471-148919
α-helix1498-152427
α-helix1527-15304
α-helix1536-155419
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-strand162415
α-helix1625-16262
α-helix1641-165212
α-helix1657-16637
β-strand1668-166926
β-strand167015
α-helix16711
β-strand1678-167926
α-helix1684-170825
α-helix1711-17144
α-helix1723-173210
α-helix1748-17558
α-helix1793-180210
α-helix1813-182715
α-helix1837-18448
Chain B: 42 helices, 59 β-strands
ElementResiduesLengthSheet
α-helix30-5223
α-helix54-6310
α-helix65-673
β-strand68-7257
α-helix75-10935
β-strand122-12438
β-strand125-12629
β-strand142-14438
α-helix1491
β-strand150-151210
β-strand158-159210
β-strand160111
β-strand165-16629
α-helix177-1859
α-helix187-19913
β-strand206-21059
β-strand216-21729
β-strand220111
β-strand229112
β-strand232112
α-helix238-2403
α-helix242-2476
β-strand253113
β-strand256-258314
α-helix262-2643
α-helix267-28014
β-strand288-289213
β-strand291-294414
β-strand298-300314
β-strand308-309213
α-helix312-32312
α-helix333-34311
β-strand356113
β-strand357-362614
α-helix370-3767
β-strand383-389714
α-helix397-4059
β-strand409-413514
α-helix419-43012
α-helix432-4365
β-strand445-44629
α-helix447-4493
β-strand450-45129
β-strand458-467109
β-strand484-493109
α-helix494-4974
α-helix498-5003
β-strand511-515515
β-strand520116
β-strand523115
α-helix531-5333
β-strand560116
α-helix561-5644
α-helix570-57910
β-strand584-588515
β-strand591-593317
β-strand600-602317
β-strand605-611715
β-strand618-622515
α-helix625-6284
β-strand629-63357
α-helix640-6456
β-strand658118
β-strand667119
α-helix671-6722
α-helix676-68813
β-strand697119
α-helix699-71517
α-helix716-7205
β-strand729-736818
β-strand743118
α-helix748-7514
α-helix758-7603
α-helix762-7698
β-strand774-776318
α-helix777-7793
β-strand792-797618
β-strand801-802220
β-strand805-806220
β-strand810-816718
α-helix818-82710
α-helix828-8303
β-strand851-853321
α-helix855-8573
β-strand858122
β-strand859-862421
α-helix868-8703
β-strand874122
α-helix875-8784
α-helix880-8889
β-strand892-896523
β-strand899-904624
β-strand972-977624
β-strand979-983523
β-strand989-994621
β-strand1001-1007721
α-helix10081
β-strand1014-1016321
β-strand1036-1038324
α-helix1043-10464
α-helix1050-10523
Chain D: 9 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix230-2312
β-strand232-235425
α-helix243-25917
β-strand264-265226
β-strand268127
α-helix273-2753
α-helix306-3138
β-strand318-319226
β-strand320-321225
β-strand322127
β-strand340-344525
α-helix349-35810
α-helix362-3665
α-helix367-37812
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
>7VFV_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
>7VFV_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
>7VFV_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
6IX(2~{S})-~{N}-[(2~{S})-1-(~{tert}-butylamino)-1-oxidanylidene-3-(4-phenylmethoxy…C38 H53 N3 O31
CACalcium ionCa2
PT5[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4…C47 H85 O19 P31
Y01Cholesterol hemisuccinateC31 H50 O43
R16HexadecaneC16 H3416
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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