7K18: Cardiac Sodium channel with toxin bound

Cardiac Sodium channel with toxin bound. Determined by electron microscopy at 3.3 Å resolution. Released 20 Jan 2021.

Method
Electron microscopy
Resolution
3.3 Å
Organisms
Rattus norvegicus, Aequorea victoria, Leiurus hebraeus
Chains
2
Atoms
9,749
Mol. weight
225.66 kDa
Ligands
NAG, 6OU
Released
20 Jan 2021

Explore 7K18 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7K18 contains 63 α-helices and 15 β-strands across 2 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: 62 helices, 12 β-strands

ElementResiduesLengthSheet
α-helix122-1298
α-helix133-14917
α-helix156-1583
α-helix161-18020
α-helix184-1896
α-helix195-21016
α-helix221-2288
α-helix229-2335
α-helix235-25016
α-helix252-27322
β-strand280-28231
α-helix283-2842
α-helix305-3106
α-helix312-3143
β-strand31712
α-helix3181
β-strand32412
β-strand341-34331
α-helix359-37113
α-helix375-38511
α-helix388-3903
α-helix391-3966
α-helix397-4059
α-helix406-42217
α-helix701-71515
α-helix721-73515
α-helix744-77128
α-helix776-7794
α-helix781-79616
α-helix809-82113
α-helix824-83512
α-helix841-86828
α-helix870-8723
α-helix887-89913
α-helix903-91210
α-helix915-94430
α-helix1191-120414
α-helix1207-122519
α-helix1235-126935
α-helix1273-129220
α-helix1302-13054
α-helix1306-131712
α-helix1320-133011
α-helix1333-135826
β-strand136413
β-strand136714
β-strand138215
α-helix1383-13864
α-helix1387-13893
β-strand139514
β-strand139813
α-helix1408-141811
α-helix1423-14319
β-strand143815
α-helix1439-14413
α-helix1446-14483
α-helix1449-14557
α-helix1456-14627
α-helix1463-148119
α-helix1491-150313
α-helix1518-152710
α-helix1530-154617
α-helix1556-158126
α-helix1586-15883
α-helix1592-161322
α-helix1623-16319
α-helix1632-16387
α-helix1644-168037
α-helix1684-16863
β-strand168716
β-strand169016
α-helix1699-171012
α-helix1715-17239
α-helix1747-177832
Chain B: 1 helix, 3 β-strands
ElementResiduesLengthSheet
β-strand2-547
α-helix24-307
β-strand36-4057
β-strand44-5297

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel protein type 5 subunit alpha, Enhanced Green fluorescent proteinAprotein1838Rattus norvegicus, Aequorea victoriaP15389 (AlphaFold model), P42212 (AlphaFold model)
Alpha-like toxin Lqh3Bprotein67Leiurus hebraeusP56678 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>7K18_1 Sodium channel protein type 5 subunit alpha, Enhanced Green fluorescent protein (chains A)
MANLLLPRGTSSFRRFTRESLAAIEKRMAEKQARGGSATSQESREGLQEEEAPRPQLDLQ
ASKKLPDLYGNPPRELIGEPLEDLDPFYSTQKTFIVLNKGKTIFRFSATNALYVLSPFHP
VRRAAVKILVHSLFSMLIMCTILTNCVFMAQHDPPPWTKYVEYTFTAIYTFESLVKILAR
GFCLHAFTFLRDPWNWLDFSVIVMAYTTEFVDLGNVSALRTFRVLRALKTISVISGLKTI
VGALIQSVKKLADVMVLTVFCLSVFALIGLQLFMGNLRHKCVRNFTELNGTNGSVEADGL
VWNSLDVYLNDPANYLLKNGTTDVLLCGNSSDAGTCPEGYRCLKAGENPDHGYTSFDSFA
WAFLALFRLMTQDCWERLYQQTLRSAGKIYMIFFMLVIFLGSFYLVNLILAVVAMAYEEQ
NQATIAETEEKEKRFQEAMEMLKKEHEALTIRGVDTVSRSSARQRALSAVSVLTSALEEL
EESHRKCPPCWNRFAQHYLIWECCPLWMSIKQKVKFVVMDPFADLTITMCIVLNTLFMAL
EHYNMTAEFEEMLQVGNLVFTGIFTAEMTFKIIALDPYYYFQQGWNIFDSIIVILSLMEL
GLSRMGNLSVLRSFRLLRVFKLAKSWPTLNTLIKIIGNSVGALGNLTLVLAIIVFIFAVV
GMQLFGKNYSELRHRISDSGLLPRWHMMDFFHAFLIIFRILCGEWIETMWDCMEVSGQSL
CLLVFLLVMVIGNLVVLNLFLALLLSSFSADNLTAPDEDGEMNNLQLALARIQRGLRFVK
RTTWDFCCGILRRRPKKPAALATHSQLPSCITAPRSPPPPEVEKVPPARKETRFEEDKRP
GQGTPGDSEPVCVPIAVAESDTEDQEEDEENGKVWWRLRKTCYRIVEHSWFETFIIFMIL
LSSGALAFEDIYLEERKTIKVLLEYADKMFTYVFVLEMLLKWVAYGFKKYFTNAWCWLDF
LIVDVSLVSLVANTLGFAEMGPIKSLRTLRALRPLRALSRFEGMRVVVNALVGAIPSIMN
VLLVCLIFWLIFSIMGVNLFAGKFGRCINQTEGDLPLNYTIVNNKSECESFNVTGELYWT
KVKVNFDNVGAGYLALLQVATFKGWMDIMYAAVDSRGYEEQPQWEDNLYMYIYFVVFIIF
GSFFTLNLFIGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPLNK
YQGFIFDIVTKQAFDVTIMFLICLNMVTMMVETDDQSPEKVNILAKINLLFVAIFTGECI
VKMAALRHYYFTNSWNIFDFVVVILSIVGTVLSDIIQKYFFSPTLFRVIRLARIGRILRL
IRGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYSIFGMANFAYVKWEAGIDDMFNFQT
FANSMLCLFQITTSAGWDGLLSPILNTGPPYCDPNLPNSNGSRGNCGSPAVGILFFTTYI
IISFLIVVNMYIAIILENFSVATEESTEPLSEDDFDMFYEIWEKFDPEATQFIEYLALSD
FADALSEPLRIAKPNQISLINMDLPMVSGDRIHCMDILFAFTKRVLGESGEMDALKIQME
EKFMAANPSKISYEPITTTLEVLFQGPGSMVSKGEELFTGVVPILVELDGDVNGHKFSVS
GEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPE
GYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNV
YIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKD
PNEKRDHMVLLEFVTAAGITLGMDELYKGSDYKDDDDK
Sequence of entity 2 (B), FASTA
>7K18_2 Alpha-like toxin Lqh3 (chains B)
VRDGYIAQPENCVYHCFPGSSGCDTLCKEKGGTSGHCGFKVGHGLACWCNALPDNVGIIV
EGEKCHS

Ligands and cofactors

IDNameFormulaCopies
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O61
6OU[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-y…C39 H76 N O8 P11

Primary citation

Structural basis for voltage-sensor trapping of the cardiac sodium channel by a deathstalker scorpion toxin. Jiang, D., Tonggu, L., Gamal El-Din, T.M. et al. Nat Commun (2021) 12:128-128. DOI 10.1038/s41467-020-20078-3 · PubMed

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

Browse structure collections

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