8VYJ: Sodium channel protein type 5 subunit alpha

Structure of full-length human cardiac sodium channel - Class-I. Determined by electron microscopy at 3.6 Å resolution. Released 12 Feb 2025.

Method
Electron microscopy
Resolution
3.6 Å
Organism
Homo sapiens
Chains
1
Atoms
11,715
Mol. weight
234.97 kDa
Ligands
6OU, Y01, NAG
Released
12 Feb 2025

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

Secondary structure: helices and β-sheets

8VYJ contains 75 α-helices and 17 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: 75 helices, 17 β-strands

ElementResiduesLengthSheet
α-helix22-287
α-helix31-355
β-strand7911
α-helix86-883
β-strand92-9541
β-strand103-10641
α-helix119-12911
α-helix132-14716
α-helix157-17923
α-helix195-20612
α-helix207-2093
α-helix211-2133
α-helix219-2213
α-helix225-2317
α-helix234-24411
α-helix253-26917
β-strand278-28252
β-strand294-29633
β-strand299-30133
α-helix311-3133
β-strand339-34352
α-helix346-3472
α-helix349-3513
α-helix358-37013
α-helix375-38511
α-helix387-3893
α-helix390-3978
α-helix398-4025
α-helix403-43230
α-helix689-6946
α-helix706-7138
α-helix716-7205
α-helix721-73515
α-helix743-77028
α-helix773-7764
α-helix781-79717
α-helix811-8199
α-helix825-83410
α-helix840-86122
α-helix862-8643
α-helix876-8772
α-helix884-89613
α-helix900-9056
α-helix915-94228
α-helix1163-11653
α-helix1172-11743
α-helix1186-120318
α-helix1205-122016
α-helix1221-12244
α-helix1227-12293
α-helix1236-126025
α-helix1270-129021
α-helix1299-13046
α-helix1305-131410
α-helix1320-13289
α-helix1331-135525
β-strand1362-136544
β-strand137214
β-strand138015
α-helix1381-13866
β-strand1393-139644
α-helix1405-141612
α-helix1421-14299
β-strand143615
α-helix1444-14463
α-helix1447-145711
α-helix1460-148021
α-helix1489-149911
α-helix1515-15195
α-helix1522-15265
α-helix1528-154619
α-helix1554-157623
α-helix1593-15953
α-helix1596-16005
α-helix1601-161010
α-helix1620-16267
α-helix1627-163913
α-helix1643-167533
β-strand168916
β-strand169216
α-helix1697-170711
α-helix1714-17174
α-helix1745-177632
α-helix1792-180110
β-strand1808-180927
α-helix1811-18177
α-helix1829-18335
α-helix1834-18374
β-strand1842-184327
β-strand1847-184937
α-helix1850-185910
α-helix1869-188113

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel protein type 5 subunit alphaAprotein2016Homo sapiensQ14524 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8VYJ_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:

Browse structure collections

About this viewer

MolViewer shows 8VYJ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.