7XLQ: PDB entry 7XLQ

Structure of human R-type voltage-gated CaV2.3-alpha2/delta1-beta1 channel complex in the ligand-free (apo) state. Determined by electron microscopy at 3.1 Å resolution. Released 8 Feb 2023.

Method
Electron microscopy
Resolution
3.1 Å
Organism
Homo sapiens
Chains
3
Atoms
20,132
Mol. weight
458.75 kDa
Ligands
Y01, CA, 3PE, R16
Released
8 Feb 2023

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

Secondary structure: helices and β-sheets

7XLQ contains 128 α-helices and 70 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: 79 helices, 11 β-strands

ElementResiduesLengthSheet
α-helix84-863
α-helix89-924
α-helix95-10814
α-helix119-1246
α-helix128-14518
β-strand14711
β-strand15411
α-helix155-1573
α-helix159-17416
α-helix193-1953
α-helix199-2035
α-helix205-21713
α-helix224-24320
β-strand249-25352
β-strand26712
β-strand277-28152
α-helix298-3069
α-helix311-32010
α-helix328-3358
α-helix336-3405
α-helix341-35818
α-helix361-38525
α-helix461-47212
α-helix476-4827
α-helix489-4924
α-helix502-52524
α-helix539-55921
α-helix570-58213
α-helix586-59813
α-helix604-6074
α-helix612-62514
α-helix643-65412
α-helix659-66810
α-helix678-6803
α-helix682-6887
α-helix693-71119
α-helix714-7207
α-helix724-7274
α-helix777-7848
α-helix1145-11473
α-helix1148-11514
α-helix1155-116612
α-helix1168-11714
α-helix1181-120626
α-helix1223-124220
α-helix1251-12577
α-helix1258-126710
α-helix1268-12714
α-helix1276-128611
α-helix1295-130612
α-helix1308-13114
β-strand1316-131833
β-strand1332-133544
β-strand1342-134544
β-strand1348-135033
α-helix1358-136912
α-helix1375-13828
α-helix1397-14004
α-helix1402-14076
α-helix1408-14147
α-helix1415-142410
α-helix1426-14283
α-helix1434-14374
α-helix1442-14465
α-helix1468-14758
α-helix1487-14904
α-helix1506-152520
α-helix1529-15324
α-helix1534-15374
α-helix1544-155916
α-helix1572-15754
α-helix1576-15794
α-helix1584-15896
α-helix1593-160210
α-helix1610-162920
α-helix1632-16343
α-helix1649-166012
α-helix1667-16704
α-helix1699-172224
α-helix1726-17294
α-helix1738-17403
α-helix1742-175211
β-strand176015
α-helix1763-17708
α-helix1784-17929
β-strand180215
α-helix1805-181612
α-helix1826-184217
α-helix1848-18547
α-helix1865-18706
Chain B: 10 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix230-2312
β-strand232-235423
α-helix243-25917
β-strand264-268523
α-helix273-2753
α-helix306-3138
β-strand318-322523
α-helix330-3323
β-strand340-344523
α-helix349-35810
α-helix363-3664
α-helix367-37812
α-helix382-3843
β-strand387-389323
α-helix394-41118
Chain D: 39 helices, 54 β-strands
ElementResiduesLengthSheet
α-helix30-5122
α-helix54-6310
α-helix65-673
β-strand68-7256
α-helix75-10935
β-strand122-12437
β-strand125-12628
α-helix135-1373
β-strand142-14437
α-helix1451
α-helix1491
β-strand150-15239
β-strand157-15939
β-strand160110
β-strand165-16628
β-strand167111
α-helix177-1848
α-helix188-19912
β-strand206-210511
β-strand215-217311
β-strand220110
β-strand229112
β-strand232112
α-helix238-2403
α-helix242-2487
α-helix250-2523
β-strand253-258613
α-helix262-2643
α-helix267-28014
β-strand288-294713
β-strand298-300313
β-strand308-309213
α-helix312-32211
α-helix333-34412
β-strand356-362713
α-helix370-3767
β-strand383-389713
α-helix397-4059
β-strand409-413513
α-helix419-43012
α-helix432-4365
β-strand445-446211
β-strand450-451211
β-strand458-4671011
β-strand484-4931011
α-helix494-4974
β-strand511-513314
β-strand520115
α-helix531-5333
β-strand560115
α-helix570-57910
β-strand584-589614
β-strand592-593216
β-strand600-601216
β-strand604-611814
β-strand618-624714
α-helix625-6273
β-strand629-63356
α-helix640-6456
α-helix646-6483
β-strand658117
α-helix676-68813
α-helix699-71517
α-helix716-7216
β-strand729-736817
β-strand743117
α-helix748-7514
α-helix758-7603
α-helix762-7698
β-strand773118
β-strand774-776317
α-helix777-7793
β-strand792-797617
β-strand800-802319
β-strand805-807319
β-strand810-816717
α-helix818-8258
β-strand849-854620
β-strand858121
β-strand859-862420
α-helix867-8704
β-strand874121
α-helix875-8773
α-helix880-88910
β-strand892-9041322
β-strand972-9831222
β-strand989-994620
β-strand1001-1007720
α-helix10081
β-strand1011118
β-strand1013-1019720
β-strand1036-1037222
α-helix1050-10523

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Voltage-dependent R-type calcium channel subunit alpha-1EAprotein2313Homo sapiensQ15878 (AlphaFold model)
Voltage-dependent calcium channel subunit alpha-2/delta-1Dprotein1077Homo sapiensP54289 (AlphaFold model)
Voltage-dependent L-type calcium channel subunit beta-1Bprotein598Homo sapiensQ02641 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>7XLQ_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 (D), FASTA
>7XLQ_2 Voltage-dependent calcium channel subunit alpha-2/delta-1 (chains D)
FPSAVTIKSWVDKMQEDLVTLAKTASGVNQLVDIYEKYQDLYTVEPNNARQLVEIAARDI
EKLLSNRSKALVRLALEAEKVQAAHQWREDFASNEVVYYNAKDDLDPEKNDSEPGSQRIK
PVFIEDANFGRQISYQHAAVHIPTDIYEGSTIVLNELNWTSALDEVFKKNREEDPSLLWQ
VFGSATGLARYYPASPWVDNSRTPNKIDLYDVRRRPWYIQGAASPKDMLILVDVSGSVSG
LTLKLIRTSVSEMLETLSDDDFVNVASFNSNAQDVSCFQHLVQANVRNKKVLKDAVNNIT
AKGITDYKKGFSFAFEQLLNYNVSRANCNKIIMLFTDGGEERAQEIFNKYNKDKKVRVFT
FSVGQHNYDRGPIQWMACENKGYYYEIPSIGAIRINTQEYLDVLGRPMVLAGDKAKQVQW
TNVYLDALELGLVITGTLPVFNITGQFENKTNLKNQLILGVMGVDVSLEDIKRLTPRFTL
CPNGYYFAIDPNGYVLLHPNLQPKPIGVGIPTINLRKRRPNIQNPKSQEPVTLDFLDAEL
ENDIKVEIRNKMIDGESGEKTFRTLVKSQDERYIDKGNRTYTWTPVNGTDYSLALVLPTY
SFYYIKAKLEETITQARYSETLKPDNFEESGYTFIAPRDYCNDLKISDNNTEFLLNFNEF
IDRKTPNNPSCNADLINRVLLDAGFTNELVQNYWSKQKNIKGVKARFVVTDGGITRVYPK
EAGENWQENPETYEDSFYKRSLDNDNYVFTAPYFNKSGPGAYESGIMVSKAVEIYIQGKL
LKPAVVGIKIDVNSWIENFTKTSIRDPCAGPVCDCKRNSDVMDCVILDDGGFLLMANHDD
YTNQIGRFFGEIDPSLMRHLVNISVYAFNKSYDYQSVCEPGAAPKQGAGHRSAYVPSVAD
ILQIGWWATAAAWSILQQFLLSLTFPRLLEAVEMEDDDFTASLSKQSCITEQTQYFFDND
SKSFSGVLDCGNCSRIFHGEKLMNTNLIFIMVESKGTCPCDTRLLIQAEQTSDGPNPCDM
VKQPRYRKGPDVCFDNNVLEDYTDCGGVSGLNPSLWYIIGIQFLLLWLVSGSTHRLL
Sequence of entity 3 (B), FASTA
>7XLQ_3 Voltage-dependent L-type calcium channel subunit beta-1 (chains B)
MVQKTSMSRGPYPPSQEIPMEVFDPSPQGKYSKRKGRFKRSDGSTSSDTTSNSFVRQGSA
ESYTSRPSDSDVSLEEDREALRKEAERQALAQLEKAKTKPVAFAVRTNVGYNPSPGDEVP
VQGVAITFEPKDFLHIKEKYNNDWWIGRLVKEGCEVGFIPSPVKLDSLRLLQEQKLRQNR
LGSSKSGDNSSSSLGDVVTGTRRPTPPASAKQKQKSTEHVPPYDVVPSMRPIILVGPSLK
GYEVTDMMQKALFDFLKHRFDGRISITRVTADISLAKRSVLNNPSKHIIIERSNTRSSLA
EVQSEIERIFELARTLQLVALDADTINHPAQLSKTSLAPIIVYIKITSPKVLQRLIKSRG
KSQSKHLNVQIAASEKLAQCPPEMFDIILDENQLEDACEHLAEYLEAYWKATHPPSSTPP
NPLLNRTMATAALAASPAPVSNLQGPYLASGDQPLERATGEHASMHEYPGELGQPPGLYP
SSHPPGRAGTLRALSRQDTFDADTPGSRNSAYTELGDSCVDMETDPSEGPGLGDPAGGGT
PPARQGSWEDEEEDYEEELTDNRNRGRNKARYCAEGGGPVLGRNKNELEGWGRGVYIR

Ligands and cofactors

IDNameFormulaCopies
Y01Cholesterol hemisuccinateC31 H50 O46
CACalcium ionCa2
3PE1,2-Distearoyl-sn-glycerophosphoethanolamineC41 H82 N O8 P1
R16HexadecaneC16 H347
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O68

Primary citation

Molecular insights into the gating mechanisms of voltage-gated calcium channel Ca V 2.3. Gao, Y., Xu, S., Cui, X. et al. Nat Commun (2023) 14:516-516. DOI 10.1038/s41467-023-36260-2 · 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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