8T6L: PDB entry 8T6L

Cryo-EM structure of rat cardiac sodium channel NaV1.5 with batrachotoxin analog BTX-B. Determined by electron microscopy at 3.3 Å resolution. Released 6 Mar 2024.

Method
Electron microscopy
Resolution
3.3 Å
Organisms
Rattus norvegicus, Aequorea victoria
Chains
1
Atoms
10,988
Mol. weight
231.78 kDa
Ligands
YIJ, 9Z9, Y01, LBN
Released
6 Mar 2024

Explore 8T6L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T6L contains 73 α-helices and 26 β-strands across 1 chain. 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, 26 β-strands

ElementResiduesLengthSheet
β-strand1511
α-helix18-3114
α-helix57-593
β-strand63-6422
α-helix65-662
α-helix67-693
α-helix71-733
β-strand81-8221
β-strand93-9641
β-strand102-10322
β-strand104-10741
β-strand11113
β-strand11513
α-helix120-13011
α-helix132-14817
α-helix156-1583
α-helix159-18022
α-helix189-1913
α-helix195-20915
α-helix217-22812
α-helix229-2335
α-helix235-24915
α-helix252-27221
α-helix276-2783
β-strand280-28344
α-helix2841
β-strand286-28725
α-helix2881
β-strand295-29625
β-strand301-30225
α-helix305-3106
β-strand31716
α-helix3181
β-strand32416
α-helix325-3262
β-strand340-34344
α-helix350-3523
α-helix359-37113
α-helix375-38511
α-helix388-3903
α-helix391-3966
α-helix397-4037
α-helix404-43431
α-helix701-71616
α-helix718-73417
β-strand73917
α-helix744-77128
α-helix774-7785
α-helix781-79919
α-helix808-82114
α-helix824-83714
α-helix841-86121
α-helix863-8686
α-helix870-8723
α-helix887-89812
α-helix903-9108
α-helix915-94329
α-helix1191-120515
α-helix1207-122418
α-helix1235-126228
α-helix1265-12695
α-helix1272-129221
α-helix1299-13068
α-helix1307-13159
α-helix1320-133112
α-helix1333-135725
β-strand1363-136758
β-strand1371-137448
α-helix1375-13762
β-strand138219
α-helix1383-13886
β-strand1395-139958
β-strand140617
α-helix1407-141913
α-helix1424-14307
β-strand143819
α-helix1446-14483
α-helix1449-14557
α-helix1456-14627
α-helix1463-148119
α-helix1491-150313
α-helix1508-15158
α-helix1519-152810
α-helix1530-154819
α-helix1556-158429
α-helix1593-161624
α-helix1618-16203
α-helix1623-16297
α-helix1632-16354
α-helix1636-16394
α-helix1643-168038
α-helix1684-16863
β-strand1687110
β-strand1690110
α-helix1699-171012
α-helix1715-17239
β-strand1735111
β-strand1741111
α-helix1747-177933

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel protein type 5 subunit alpha,Green fluorescent proteinAprotein1874Rattus norvegicus, Aequorea victoriaP15389 (AlphaFold model), P42212 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8T6L_1 Sodium channel protein type 5 subunit alpha,Green fluorescent protein (chains A)
MANLLLPRGTSSFRRFTRESLAAIEKRMAEKQTRGGSATSQESREGLQEEEAPRPQLDLQ
ASKKLPDLYGNPPRELIGEPLEDLDPFYSTQKTFIVLNKGKTIFRFSATNALYVLSPFHP
VRRAAVKILVHSLFSMLIMCTILTNCVFMAQHDPPPWTKYVEYTFTAIYTFESLVKILAR
GFCLHAFTFLRDPWNWLDFSVIVMAYTTEFVDLDNVSALRTFRVLRALKTISVISGLKTI
VGALIQSVKKLADVMVLTVFCLSVFALIGLQLFMGNLRHKCVRNFTELNGTNGSVEADGL
VWNSLDVYLNDPANYLLKNGTTDVLLCGNSSDAGTCPEGYRCLKAGENPDHGYTSFDSFA
WAFLALFRLMTQDCWERLYQQTLRSAGKIYMIFFMLVIFLGSFYLVNLILAVVAMAYEEQ
NQATIAETEEKEKRFQEAMEMLKKEHEALTIRGVDTVSRSSRQRALSAVSVLTSALEELE
ESHRKCPPCWNRFAQHYLIWECCPLWMSIKQKVKFVVMDPFADLTITMCIVLNTLFMALE
HYNMTAEFEEMLQVGNLVFTGIFTAEMTFKIIALDPYYYFQQGWNIFDSIIVILSLMELG
LSRMGNLSVLRSFRLLRVFKLAKSWPTLNTLIKIIGNSVGALGNLTLVLAIIVFIFAVVG
MQLFGKNYSELRHRISDSGLLPRWHMMDFFHAFLIIFRILCGEWIETMWDCMEVSGQSLC
LLVFLLVMVIGNLVVLNLFLALLLSSFSADNLTAPDEDGEMNNLQLALARIQRGLRFVKR
TTWDFCCGILRRRPKKPAALATHSQLPSCITAPRSPPPPEVEKVPPARKETRFEEDKRPG
QGTPGDSEPVCVPIAVAESDTEDQEEDEENSGKVWWRLRKTCYRIVEHSWFETFIIFMIL
LSSGALAFEDIYLEERKTIKVLLEYADKMFTYVFVLEMLLKWVAYGFKKYFTNAWCWLDF
LIVDVSLVSLVANTLGFAEMGPIKSLRTLRALRPLRALSRFEGMRVVVNALVGAIPSIMN
VLLVCLIFWLIFSIMGVNLFAGKFGRCINQTEGDLPLNYTIVNNKSECESFNVTGELYWT
KVKVNFDNVGAGYLALLQVATFKGWMDIMYAAVDSRGYEEQPQWEDNLYMYIYFVVFIIF
GSFFTLNLFIGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPLNK
YQGFIFDIVTKQAFDVTIMFLICLNMVTMMVETDDQSPEKVNILAKINLLFVAIFTGECI
VKMAALRHYYFTNSWNIFDFVVVILSIVGTVLSDIIQKYFFSPTLFRVIRLARIGRILRL
IRGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYSIFGMANFAYVKWEAGIDDMFNFQT
FANSMLCLFQITTSAGWDGLLSPILNTGPPYCDPNLPNSNGSRGNCGSPAVGILFFTTYI
IISFLIVVNMYIAIILENFSVATEESTEPLSEDDFDMFYEIWEKFDPEATQFIEYLALSD
FADALSEPLRIAKPNQISLINMDLPMVSGDRIHCMDILFAFTKRVLGESGEMDALKIQME
EKFMAANPSKISYEPITTTLRRKHEEVSATVIQRAFRRHLLQRSVKHASFLFRVDLEVLF
QGPGSMVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLP
VPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKF
EGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDG
SVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMD
ELYKGSDYKDDDDK

Ligands and cofactors

IDNameFormulaCopies
YIJ(1R)-1-[(5aR,7aR,9R,11aS,11bS,12R,13aR)-9,12-dihydroxy-2,11a-dimethyl-1,2,3,4,7…C31 H39 N O62
9Z9(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-enC34 H56 O52
Y01Cholesterol hemisuccinateC31 H50 O411
LBN1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholineC42 H82 N O8 P10
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O63

Primary citation

Dual receptor-sites reveal the structural basis for hyperactivation of sodium channels by poison-dart toxin batrachotoxin. Tonggu, L., Wisedchaisri, G., Gamal El-Din, T.M. et al. Nat Commun (2024) 15:2306-2306. DOI 10.1038/s41467-024-45958-w · PubMed

Other PDB entries of the same protein (UniProt P15389 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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