7YG5: PDB entry 7YG5

Structure of human R-type voltage-gated CaV2.3-alpha2/delta1-beta1 channel complex in the topiramate-bound state. Determined by electron microscopy at 3.0 Å resolution. Released 29 Nov 2023.

Method
Electron microscopy
Resolution
3.0 Å
Organism
Homo sapiens
Chains
3
Atoms
20,308
Mol. weight
463.73 kDa
Ligands
Y01, R16, 3PE, CA
Released
29 Nov 2023

Explore 7YG5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YG5 contains 123 α-helices and 63 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: 75 helices, 7 β-strands

ElementResiduesLengthSheet
α-helix95-10814
α-helix119-1246
α-helix128-14417
α-helix159-17416
α-helix178-1803
α-helix190-1989
α-helix199-2035
α-helix205-21713
α-helix219-2213
α-helix224-24219
β-strand249-25351
β-strand26711
β-strand277-28151
α-helix298-3069
α-helix311-32212
α-helix328-3358
α-helix336-3416
α-helix342-35716
α-helix361-38424
α-helix461-4644
α-helix468-4725
α-helix476-49217
α-helix502-52726
α-helix539-55921
α-helix570-58213
α-helix586-59813
α-helix601-62525
α-helix643-65412
α-helix659-66911
α-helix677-6815
α-helix697-71216
α-helix724-7274
α-helix777-78711
α-helix1147-11504
α-helix1158-117114
α-helix1181-120828
α-helix1223-124119
α-helix1251-12577
α-helix1259-12635
α-helix1265-12673
α-helix1268-12714
α-helix1273-128816
α-helix1293-131119
β-strand1316-131832
β-strand1332-133543
β-strand1342-134543
β-strand1348-135032
α-helix1358-136912
α-helix1374-13829
α-helix1397-14004
α-helix1402-14098
α-helix1410-14145
α-helix1415-142410
α-helix1426-14283
α-helix1434-14374
α-helix1442-14465
α-helix1467-14693
α-helix1471-14755
α-helix1481-149414
α-helix1505-152521
α-helix1529-15324
α-helix1534-15374
α-helix1543-156018
α-helix1575-15806
α-helix1581-15844
α-helix1585-15884
α-helix1593-160513
α-helix1610-162920
α-helix1632-16343
α-helix1649-166012
α-helix1665-16717
α-helix1699-172224
α-helix1723-17253
α-helix1726-17294
α-helix1738-17414
α-helix1743-17519
α-helix1762-17676
α-helix1784-17907
α-helix1805-181713
α-helix1825-184218
α-helix1848-18547
α-helix1863-18642
Chain B: 9 helices, 5 β-strands
ElementResiduesLengthSheet
β-strand232-23544
α-helix243-25917
β-strand264-26854
α-helix273-2753
α-helix304-31310
β-strand318-32254
α-helix330-3323
β-strand340-34454
α-helix349-35810
α-helix362-3665
α-helix367-37812
α-helix382-3843
β-strand387-38934
α-helix394-41118
Chain D: 39 helices, 51 β-strands
ElementResiduesLengthSheet
α-helix30-5122
α-helix54-6310
α-helix65-673
β-strand68-7255
α-helix75-10935
β-strand123-12426
β-strand125-12627
α-helix135-1373
β-strand143-14426
β-strand150-15128
β-strand158-15928
β-strand165-16737
α-helix177-1859
α-helix189-19911
β-strand206-21057
β-strand215-21737
α-helix238-2403
α-helix242-2476
β-strand25319
β-strand256-259410
α-helix262-2643
α-helix267-28014
β-strand288-28929
β-strand291-294410
β-strand298-300310
β-strand308-30929
α-helix312-32211
α-helix333-34311
β-strand35619
β-strand357-362610
α-helix370-3756
β-strand383-389710
α-helix397-4059
β-strand409-413510
α-helix419-43012
α-helix432-4365
β-strand445-44627
α-helix447-4493
β-strand450-45127
β-strand458-467107
β-strand484-493107
α-helix494-4985
β-strand511-515511
β-strand520112
β-strand521-523311
α-helix531-5333
β-strand560112
α-helix569-58012
β-strand584-588511
β-strand591-593313
β-strand600-602313
β-strand605-611711
β-strand618-624711
α-helix625-6273
β-strand629-63355
α-helix640-6456
α-helix646-6483
β-strand658114
α-helix676-68813
α-helix691-6933
α-helix699-71517
α-helix716-7216
β-strand729-736814
β-strand743114
α-helix748-7514
α-helix758-7603
α-helix762-7698
β-strand774-776314
α-helix777-7793
β-strand792-797614
β-strand800-802315
β-strand805-807315
β-strand810-816714
α-helix818-8258
β-strand849-854616
β-strand858117
β-strand861-862216
β-strand874117
α-helix875-8773
α-helix880-88910
β-strand892-9041318
α-helix905-9084
β-strand972-9831218
β-strand989-996816
β-strand999-1007916
α-helix10081
β-strand1013-1018616
β-strand1036-1037218
α-helix1043-10464
α-helix1050-10523

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Voltage-dependent R-type calcium channel subunit alpha-1EAprotein2313Homo sapiensQ15878 (AlphaFold model)
Voltage-dependent L-type calcium channel subunit beta-1Bprotein598Homo sapiensQ02641 (AlphaFold model)
Voltage-dependent calcium channel subunit alpha-2/delta-1Dprotein1103Homo sapiensP54289 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>7YG5_1 Voltage-dependent R-type calcium channel subunit alpha-1E (chains A)
MARFGEAVVARPGSGDGDSDQSRNRQGTPVPASGQAAAYKQTKAQRARTMALYNPIPVRQ
NCFTVNRSLFIFGEDNIVRKYAKKLIDWPPFEYMILATIIANCIVLALEQHLPEDDKTPM
SRRLEKTEPYFIGIFCFEAGIKIVALGFIFHKGSYLRNGWNVMDFIVVLSGILATAGTHF
NTHVDLRTLRAVRVLRPLKLVSGIPSLQIVLKSIMKAMVPLLQIGLLLFFAILMFAIIGL
EFYSGKLHRACFMNNSGILEGFDPPHPCGVQGCPAGYECKDWIGPNDGITQFDNILFAVL
TVFQCITMEGWTTVLYNTNDALGATWNWLYFIPLIIIGSFFVLNLVLGVLSGEFAKERER
VENRRAFMKLRRQQQIERELNGYRAWIDKAEEVMLAEENKNAGTSALEVLRRATIKRSRT
EAMTRDSSDEHCVDISSVGTPLARASIKSAKVDGVSYFRHKERLLRISIRHMVKSQVFYW
IVLSLVALNTACVAIVHHNQPQWLTHLLYYAEFLFLGLFLLEMSLKMYGMGPRLYFHSSF
NCFDFGVTVGSIFEVVWAIFRPGTSFGISVLRALRLLRIFKITKYWASLRNLVVSLMSSM
KSIISLLFLLFLFIVVFALLGMQLFGGRFNFNDGTPSANFDTFPAAIMTVFQILTGEDWN
EVMYNGIRSQGGVSSGMWSAIYFIVLTLFGNYTLLNVFLAIAVDNLANAQELTKDEQEEE
EAFNQKHALQKAKEVSPMSAPNMPSIERDRRRRHHMSMWEPRSSHLRERRRRHHMSVWEQ
RTSQLRKHMQMSSQEALNREEAPTMNPLNPLNPLSSLNPLNAHPSLYRRPRAIEGLALGL
ALEKFEEERISRGGSLKGDGGDRSSALDNQRTPLSLGQREPPWLARPCHGNCDPTQQEAG
GGEAVVTFEDRARHRQSQRRSRHRRVRTEGKESSSASRSRSASQERSLDEAMPTEGEKDH
ELRGNHGAKEPTIQEERAQDLRRTNSLMVSRGSGLAGGLDEADTPLVLPHPELEVGKHVV
LTEQEPEGSSEQALLGNVQLDMGRVISQSEPDLSCITANTDKATTESTSVTVAIPDVDPL
VDSTVVHISNKTDGEASPLKEAEIREDEEEVEKKKQKKEKRETGKAMVPHSSMFIFSTTN
PIRRACHYIVNLRYFEMCILLVIAASSIALAAEDPVLTNSERNKVLRYFDYVFTGVFTFE
MVIKMIDQGLILQDGSYFRDLWNILDFVVVVGALVAFALANALGTNKGRDIKTIKSLRVL
RVLRPLKTIKRLPKLKAVFDCVVTSLKNVFNILIVYKLFMFIFAVIAVQLFKGKFFYCTD
SSKDTEKECIGNYVDHEKNKMEVKGREWKRHEFHYDNIIWALLTLFTVSTGEGWPQVLQH
SVDVTEEDRGPSRSNRMEMSIFYVVYFVVFPFFFVNIFVALIIITFQEQGDKMMEECSLE
KNERACIDFAISAKPLTRYMPQNRHTFQYRVWHFVVSPSFEYTIMAMIALNTVVLMMKYY
SAPCTYELALKYLNIAFTMVFSLECVLKVIAFGFLNYFRDTWNIFDFITVIGSITEIILT
DSKLVNTSGFNMSFLKLFRAARLIKLLRQGYTIRILLWTFVQSFKALPYVCLLIAMLFFI
YAIIGMQVFGNIKLDEESHINRHNNFRSFFGSLMLLFRSATGEAWQEIMLSCLGEKGCEP
DTTAPSGQNENERCGTDLAYVYFVSFIFFCSFLMLNLFVAVIMDNFEYLTRDSSILGPHH
LDEFVRVWAEYDRAACGRIHYTEMYEMLTLMSPPLGLGKRCPSKVAYKRLVLMNMPVAED
MTVHFTSTLMALIRTALDIKIAKGGADRQQLDSELQKETLAIWPHLSQKMLDLLVPMPKA
SDLTVGKIYAAMMIMDYYKQSKVKKQRQQLEEQKNAPMFQRMEPSSLPQEIIANAKALPY
LQQDPVSGLSGRSGYPSMSPLSPQDIFQLACMDPADDGQFQERQSLEPEVSELKSVQPSN
HGIYLPSDTQEHAGSGRASSMPRLTVDPQVVTDPSSMRRSFSTIRDKRSNSSWLEEFSME
RSSENTYKSRRRSYHSSLRLSAHRLNSDSGHKSDTHRSGGRERGRSKERKHLLSPDVSRC
NSEERGTQADWESPERRQSRSPSEGRSQTPNRQGTGSLSESSIPSVSDTSTPRRSRRQLP
PVPPKPRPLLSYSSLIRHAGSISPPADGSEEGSPLTSQALESNNACLTESSNSPHPQQSQ
HASPQRYISEPYLALHEDSHASDCGEEETLTFEAAVATSLGRSNTIGSAPPLRHSWQMPN
GHYRRRRRGGPGPGMMCGAVNNLLSDTEEDDKC
Sequence of entity 2 (B), FASTA
>7YG5_2 Voltage-dependent L-type calcium channel subunit beta-1 (chains B)
MVQKTSMSRGPYPPSQEIPMEVFDPSPQGKYSKRKGRFKRSDGSTSSDTTSNSFVRQGSA
ESYTSRPSDSDVSLEEDREALRKEAERQALAQLEKAKTKPVAFAVRTNVGYNPSPGDEVP
VQGVAITFEPKDFLHIKEKYNNDWWIGRLVKEGCEVGFIPSPVKLDSLRLLQEQKLRQNR
LGSSKSGDNSSSSLGDVVTGTRRPTPPASAKQKQKSTEHVPPYDVVPSMRPIILVGPSLK
GYEVTDMMQKALFDFLKHRFDGRISITRVTADISLAKRSVLNNPSKHIIIERSNTRSSLA
EVQSEIERIFELARTLQLVALDADTINHPAQLSKTSLAPIIVYIKITSPKVLQRLIKSRG
KSQSKHLNVQIAASEKLAQCPPEMFDIILDENQLEDACEHLAEYLEAYWKATHPPSSTPP
NPLLNRTMATAALAASPAPVSNLQGPYLASGDQPLERATGEHASMHEYPGELGQPPGLYP
SSHPPGRAGTLRALSRQDTFDADTPGSRNSAYTELGDSCVDMETDPSEGPGLGDPAGGGT
PPARQGSWEDEEEDYEEELTDNRNRGRNKARYCAEGGGPVLGRNKNELEGWGRGVYIR
Sequence of entity 3 (D), FASTA
>7YG5_3 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

Ligands and cofactors

IDNameFormulaCopies
Y01Cholesterol hemisuccinateC31 H50 O49
R16HexadecaneC16 H346
3PE1,2-Distearoyl-sn-glycerophosphoethanolamineC41 H82 N O8 P2
CACalcium ionCa2
TOR[(3aS,5aR,8aR,8bS)-2,2,7,7-tetramethyltetrahydro-3aH-bis[1,3]dioxolo[4,5-b:4',5…C12 H21 N O8 S1
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O68

Primary citation

Structural insights into the allosteric effects of the antiepileptic drug topiramate on the Ca V 2.3 channel. Gao, Y., Bai, Q., Zhang, X.C. et al. Biochem Biophys Res Commun (2024) 725:150271-150271. DOI 10.1016/j.bbrc.2024.150271 · PubMed

Other PDB entries of the same protein (UniProt Q15878 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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