8VYK: Sodium channel protein type 5 subunit alpha

Structure of full-length human cardiac sodium channel - Class-II. Determined by electron microscopy at 3.9 Å resolution. Released 12 Feb 2025.

Method
Electron microscopy
Resolution
3.9 Å
Organism
Homo sapiens
Chains
1
Atoms
11,721
Mol. weight
234.97 kDa
Ligands
6OU, Y01, NAG
Released
12 Feb 2025

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

Secondary structure: helices and β-sheets

8VYK contains 80 α-helices and 18 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: 80 helices, 18 β-strands

ElementResiduesLengthSheet
α-helix18-258
α-helix28-303
α-helix31-355
β-strand8011
β-strand92-9651
β-strand102-10651
α-helix119-12911
α-helix131-14717
α-helix157-17923
α-helix198-20912
α-helix211-2122
α-helix221-23111
α-helix234-24916
α-helix254-26916
β-strand278-28252
α-helix283-2842
β-strand294-29633
β-strand299-30133
α-helix305-3084
α-helix311-3133
β-strand31412
α-helix3151
β-strand31614
β-strand32314
α-helix324-3252
α-helix335-3362
β-strand339-34352
α-helix346-3472
α-helix349-3513
α-helix358-37013
α-helix374-38512
α-helix387-3893
α-helix390-3978
α-helix398-4025
α-helix403-43230
α-helix689-6924
α-helix706-7138
α-helix719-73315
α-helix745-76622
α-helix773-7753
α-helix781-79515
α-helix805-81713
α-helix825-8339
α-helix834-8385
α-helix840-86122
α-helix866-8683
α-helix884-89512
α-helix900-9034
α-helix915-94228
α-helix1163-11653
α-helix1172-11754
α-helix1186-11883
α-helix1189-120315
α-helix1205-122117
α-helix1222-12243
α-helix1227-12304
α-helix1234-126027
α-helix1271-129020
α-helix1297-13015
α-helix1302-131615
α-helix1318-132710
α-helix1331-135626
β-strand1361-136555
β-strand138016
α-helix1381-13866
β-strand1393-139755
α-helix1405-141713
α-helix1421-14299
β-strand143616
α-helix1444-14463
α-helix1447-14548
α-helix1455-14595
α-helix1460-148021
α-helix1489-14979
α-helix1518-15269
α-helix1529-154416
α-helix1554-157724
α-helix1593-160614
α-helix1608-16114
α-helix1621-16266
α-helix1627-16304
α-helix1634-16374
α-helix1645-16539
α-helix1655-167521
α-helix1697-170711
α-helix1714-17174
α-helix1718-17203
α-helix1745-177531
α-helix1791-180111
β-strand1808-180927
α-helix1811-18177
α-helix1818-18203
α-helix1832-18354
β-strand184318
β-strand184718
β-strand1848-184927
α-helix1854-18596
α-helix1867-188115

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel protein type 5 subunit alphaAprotein2016Homo sapiensQ14524 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8VYK_1 Sodium channel protein type 5 subunit alpha (chains A)
MANFLLPRGTSSFRRFTRESLAAIEKRMAEKQARGSTTLQESREGLPEEEAPRPQLDLQA
SKKLPDLYGNPPQELIGEPLEDLDPFYSTQKTFIVLNKGKTIFRFSATNALYVLSPFHPI
RRAAVKILVHSLFNMLIMCTILTNCVFMAQHDPPPWTKYVEYTFTAIYTFESLVKILARG
FCLHAFTFLRDPWNWLDFSVIIMAYTTEFVDLGNVSALRTFRVLRALKTISVISGLKTIV
GALIQSVKKLADVMVLTVFCLSVFALIGLQLFMGNLRHKCVRNFTALNGTNGSVEADGLV
WESLDLYLSDPENYLLKNGTSDVLLCGNSSDAGTCPEGYRCLKAGENPDHGYTSFDSFAW
AFLALFRLMTQDCWERLYQQTLRSAGKIYMIFFMLVIFLGSFYLVNLILAVVAMAYEEQN
QATIAETEEKEKRFQEAMEMLKKEHEALTIRGVDTVSRSSLEMSPLAPVNSHERRSKRRK
RMSSGTEECGEDRLPKSDSEDGPRAMNHLSLTRGLSRTSMKPRSSRGSIFTFRRRDLGSE
ADFADDENSTAGESESHHTSLLVPWPLRRTSAQGQPSPGTSAPGHALHGKKNSTVDCNGV
VSLLGAGDPEATSPGSHLLRPVMLEHPPDTTTPSEEPGGPQMLTSQAPCVDGFEEPGARQ
RALSAVSVLTSALEELEESRHKCPPCWNRLAQRYLIWECCPLWMSIKQGVKLVVMDPFTD
LTITMCIVLNTLFMALEHYNMTSEFEEMLQVGNLVFTGIFTAEMTFKIIALDPYYYFQQG
WNIFDSIIVILSLMELGLSRMSNLSVLRSFRLLRVFKLAKSWPTLNTLIKIIGNSVGALG
NLTLVLAIIVFIFAVVGMQLFGKNYSELRDSDSGLLPRWHMMDFFHAFLIIFRILCGEWI
ETMWDCMEVSGQSLCLLVFLLVMVIGNLVVLNLFLALLLSSFSADNLTAPDEDREMNNLQ
LALARIQRGLRFVKRTTWDFCCGLLRQRPQKPAALAAQGQLPSCIATPYSPPPPETEKVP
PTRKETRFEEGEQPGQGTPGDPEPVCVPIAVAESDTDDQEEDEENSLGTEEESSKQQESQ
PVSGGPEAPPDSRTWSQVSATASSEAEASASQADWRQQWKAEPQAPGCGETPEDSCSEGS
TADMTNTAELLEQIPDLGQDVKDPEDCFTEGCVRRCPCCAVDTTQAPGKVWWRLRKTCYH
IVEHSWFETFIIFMILLSSGALAFEDIYLEERKTIKVLLEYADKMFTYVFVLEMLLKWVA
YGFKKYFTNAWCWLDFLIVDVSLVSLVANTLGFAEMGPIKSLRTLRALRPLRALSRFEGM
RVVVNALVGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGKFGRCINQTEGDLPLNYTIVNN
KSQCESLNLTGELYWTKVKVNFDNVGAGYLALLQVATFKGWMDIMYAAVDSRGYEEQPQW
EYNLYMYIYFVIFIIFGSFFTLNLFIGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKK
LGSKKPQKPIPRPLNKYQGFIFDIVTKQAFDVTIMFLICLNMVTMMVETDDQSPEKINIL
AKINLLFVAIFTGECIVKLAALRHYYFTNSWNIFDFVVVILSIVGTVLSDIIQKYFFSPT
LFRVIRLARIGRILRLIRGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYSIFGMANFA
YVKWEAGIDDMFNFQTFANSMLCLFQITTSAGWDGLLSPILNTGPPYCDPTLPNSNGSRG
DCGSPAVGILFFTTYIIISFLIVVNMYIAIILENFSVATEESTEPLSEDDFDMFYEIWEK
FDPEATQFIEYSVLSDFADALSEPLRIAKPNQISLINMDLPMVSGDRIHCMDILFAFTKR
VLGESGEMDALKIQMEEKFMAANPSKISYEPITTTLRRKHEEVSAMVIQRAFRRHLLQRS
LKHASFLFRQQAGSGLSEEDAPEREGLIAYVMSENFSRPLGPPSSSSISSTSFPPSYDSV
TRATSDNLQVRGSDYSHSEDLADFPPSPDRDRESIV

Ligands and cofactors

IDNameFormulaCopies
6OU[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-y…C39 H76 N O8 P2
Y01Cholesterol hemisuccinateC31 H50 O47
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O63

Primary citation

Structural basis of human Na v 1.5 gating mechanisms. Biswas, R., Lopez-Serrano, A.L., Purohit, A. et al. Proc Natl Acad Sci U S A (2025) 122:e2416181122-e2416181122. DOI 10.1073/pnas.2416181122 · PubMed

Other PDB entries of the same protein (UniProt Q14524 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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