8F6P: Rat Cardiac Sodium Channel with Ranolazine Bound

Rat Cardiac Sodium Channel with Ranolazine Bound. Determined by electron microscopy at 3.2 Å resolution. Released 12 Apr 2023.

Method
Electron microscopy
Resolution
3.2 Å
Organisms
Rattus norvegicus, Aequorea victoria
Chains
1
Atoms
9,278
Mol. weight
223.1 kDa
Ligands
Y01, 6OU, XHO, BMA
Released
12 Apr 2023

Explore 8F6P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F6P contains 65 α-helices and 12 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: 65 helices, 12 β-strands

ElementResiduesLengthSheet
α-helix120-13011
α-helix132-14918
α-helix156-17924
α-helix195-21016
α-helix218-22811
α-helix229-2335
α-helix235-25016
α-helix252-27221
α-helix276-2783
β-strand280-28341
β-strand28712
β-strand29512
α-helix297-2993
β-strand30212
α-helix305-3106
α-helix312-3143
β-strand31713
α-helix3181
β-strand32413
α-helix336-3372
β-strand340-34341
α-helix350-3523
α-helix359-37012
α-helix375-38511
α-helix388-3903
α-helix391-3977
α-helix398-4025
α-helix403-42927
α-helix720-73617
α-helix744-77128
α-helix774-7774
α-helix781-79717
α-helix807-8093
α-helix810-8134
α-helix814-8218
α-helix824-83613
α-helix841-86828
α-helix870-8734
α-helix887-89913
α-helix904-9129
α-helix915-94430
α-helix1194-120512
α-helix1207-122418
α-helix1236-126934
α-helix1272-129120
α-helix1302-13054
α-helix1306-131510
α-helix1320-135839
β-strand1363-136754
β-strand137414
α-helix1375-13762
β-strand138215
α-helix1383-13886
β-strand1395-139954
α-helix1408-141811
α-helix1423-14308
β-strand143815
α-helix1439-14413
α-helix1448-14558
α-helix1456-14627
α-helix1463-148119
α-helix1491-150414
α-helix1506-15083
α-helix1521-15277
α-helix1530-154819
α-helix1556-158126
α-helix1586-15905
α-helix1592-161120
α-helix1623-16297
α-helix1630-16378
α-helix1638-16414
α-helix1644-168037
α-helix1699-171012
α-helix1715-17239
α-helix1747-176115
α-helix1762-17687
α-helix1769-177911

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel protein type 5 subunit alpha,Green fluorescent proteinAprotein1838Rattus norvegicus, Aequorea victoriaP15389 (AlphaFold model), P42212 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8F6P_1 Sodium channel protein type 5 subunit alpha,Green fluorescent protein (chains A)
MANLLLPRGTSSFRRFTRESLAAIEKRMAEKQARGGSATSQESREGLQEEEAPRPQLDLQ
ASKKLPDLYGNPPRELIGEPLEDLDPFYSTQKTFIVLNKGKTIFRFSATNALYVLSPFHP
VRRAAVKILVHSLFSMLIMCTILTNCVFMAQHDPPPWTKYVEYTFTAIYTFESLVKILAR
GFCLHAFTFLRDPWNWLDFSVIVMAYTTEFVDLGNVSALRTFRVLRALKTISVISGLKTI
VGALIQSVKKLADVMVLTVFCLSVFALIGLQLFMGNLRHKCVRNFTELNGTNGSVEADGL
VWNSLDVYLNDPANYLLKNGTTDVLLCGNSSDAGTCPEGYRCLKAGQNPDHGYTSFDSFA
WAFLALFRLMTQDCWERLYQQTLRSAGKIYMIFFMLVIFLGSFYLVNLILAVVAMAYEEQ
NQATIAETEEKEKRFQEAMEMLKKEHEALTIRGVDTVSRSSARQRALSAVSVLTSALEEL
EESHRKCPPCWNRFAQHYLIWECCPLWMSIKQKVKFVVMDPFADLTITMCIVLNTLFMAL
EHYNMTAEFEEMLQVGNLVFTGIFTAEMTFKIIALDPYYYFQQGWNIFDSIIVILSLMEL
GLSRMGNLSVLRSFRLLRVFKLAKSWPTLNTLIKIIGNSVGALGNLTLVLAIIVFIFAVV
GMQLFGKNYSELRHRISDSGLLPRWHMMDFFHAFLIIFRILCGEWIETMWDCMEVSGQSL
CLLVFLLVMVIGNLVVLNLFLALLLSSFSADNLTAPDEDGEMNNLQLALARIQRGLRFVK
RTTWDFCCGILRRRPKKPAALATHSQLPSCITAPRSPPPPEVEKVPPARKETRFEEDKRP
GQGTPGDSEPVCVPIAVAESDTEDQEEDEENGKVWWRLRKTCYRIVEHSWFETFIIFMIL
LSSGALAFEDIYLEERKTIKVLLEYADKMFTYVFVLEMLLKWVAYGFKKYFTNAWCWLDF
LIVDVSLVSLVANTLGFAEMGPIKSLRTLRALRPLRALSRFEGMRVVVNALVGAIPSIMN
VLLVCLIFWLIFSIMGVNLFAGKFGRCINQTEGDLPLNYTIVNNKSECESFNVTGELYWT
KVKVNFDNVGAGYLALLQVATFKGWMDIMYAAVDSRGYEEQPQWEDNLYMYIYFVVFIIF
GSFFTLNLFIGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNMMKKLGSKKPQKPIPRPLNK
YQGFIFDIVTKQAFDVTIMFLICLNMVTMMVETDDQSPEKVNILAKINLLFVAIFTGECI
VKMAALRHYYFTNSWNIFDFVVVILSIVGTVLSDIIQKYFFSPTLFRVIRLARIGRILRL
IRGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYSIFGMANFAYVKWEAGIDDMFNFQT
FANSMLCLFQITTSAGWDGLLSPILNTGPPYCDPNLPNSNGSRGNCGSPAVGILFFTTYI
IISFLIVVNMYIAIILENFSVATEESTEPLSEDDFDMFYEIWEKFDPEATQFIEYLALSD
FADALSEPLRIAKPNQISLINMDLPMVSGDRIHCMDILFAFTKRVLGESGEMDALKIQME
EKFMAANPSKISYEPITTTLEVLFQGPGSMVSKGEELFTGVVPILVELDGDVNGHKFSVS
GEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPE
GYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNV
YIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKD
PNEKRDHMVLLEFVTAAGITLGMDELYKGSDYKDDDDK

Ligands and cofactors

IDNameFormulaCopies
Y01Cholesterol hemisuccinateC31 H50 O413
6OU[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-y…C39 H76 N O8 P6
XHO(R)-ranolazineC24 H33 N3 O41
BMAbeta-D-mannopyranoseC6 H12 O63
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O67

Primary citation

Structural basis for inhibition of the cardiac sodium channel by the atypical antiarrhythmic drug ranolazine. Lenaeus, M., Gamal El-Din, T.M., Tonggu, L. et al. Nat Cardiovasc Res (2023) 2:587-594. DOI 10.1038/s44161-023-00271-5 · 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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