6AGF: Human voltage-gated sodium channel Nav1.4

Structure of the human voltage-gated sodium channel Nav1.4 in complex with beta1. Determined by electron microscopy at 3.2 Å resolution. Released 10 Oct 2018.

Method
Electron microscopy
Resolution
3.2 Å
Organism
Homo sapiens
Chains
2
Atoms
10,980
Mol. weight
244.3 kDa
Ligands
NAG, 9Z9, 6OU
Released
10 Oct 2018

Explore 6AGF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6AGF contains 71 α-helices and 22 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: 68 helices, 7 β-strands

ElementResiduesLengthSheet
α-helix121-1288
α-helix133-14715
α-helix158-17922
α-helix184-1885
α-helix194-20916
α-helix219-2279
α-helix228-2325
α-helix236-2438
α-helix245-2484
α-helix251-27222
α-helix275-2773
β-strand279-28241
α-helix338-3425
α-helix357-3582
α-helix369-3702
β-strand373-37641
α-helix392-3976
α-helix400-4034
α-helix408-41912
α-helix421-4233
α-helix424-4296
α-helix430-4345
α-helix439-45315
α-helix455-4628
α-helix561-57616
α-helix581-59515
α-helix604-63128
α-helix641-65919
α-helix668-6703
α-helix672-6809
α-helix686-69712
α-helix703-72624
α-helix730-7323
α-helix747-75913
α-helix764-7729
α-helix775-80228
α-helix1015-102814
α-helix1031-104616
α-helix1053-10553
α-helix1060-107819
α-helix1081-10877
α-helix1090-10934
α-helix1098-111619
α-helix1130-114112
α-helix1144-115310
α-helix1157-118226
β-strand1188-119142
β-strand119712
α-helix1198-11992
β-strand120513
α-helix1206-12094
α-helix1210-12123
β-strand1218-122142
α-helix1230-124213
α-helix1246-125510
β-strand126113
α-helix1269-12713
α-helix1272-12787
α-helix1279-12857
α-helix1286-130419
α-helix1316-13249
α-helix1336-13383
α-helix1347-13504
α-helix1354-13629
α-helix1365-13717
α-helix1379-140426
α-helix1415-143925
α-helix1447-14504
α-helix1451-146313
α-helix1468-150336
α-helix1522-153110
α-helix1532-15343
α-helix1538-15425
α-helix1557-15593
α-helix1571-160535
Chain B: 3 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix25-273
β-strand29-3134
β-strand36-3835
β-strand4116
β-strand50-5127
β-strand57-6048
β-strand68-7258
β-strand80-8128
β-strand90-9235
β-strand10316
β-strand106-10835
α-helix113-1153
β-strand117-12378
β-strand126-12837
β-strand133-13537
β-strand138-14478
β-strand145-14734
α-helix155-19036

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel protein type 4 subunit alphaAprotein1879Homo sapiensP35499 (AlphaFold model)
Sodium channel subunit beta-1Bprotein218Homo sapiensQ07699 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>6AGF_1 Sodium channel protein type 4 subunit alpha (chains A)
MASWSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYKDDDDKGTMARPSLCTLVPLGPECL
RPFTRESLAAIEQRAVEEEARLQRNKQMEIEEPERKPRSDLEAGKNLPMIYGDPPPEVIG
IPLEDLDPYYSNKKTFIVLNKGKAIFRFSATPALYLLSPFSVVRRGAIKVLIHALFSMFI
MITILTNCVFMTMSDPPPWSKNVEYTFTGIYTFESLIKILARGFCVDDFTFLRDPWNWLD
FSVIMMAYLTEFVDLGNISALRTFRVLRALKTITVIPGLKTIVGALIQSVKKLSDVMILT
VFCLSVFALVGLQLFMGNLRQKCVRWPPPFNDTNTTWYSNDTWYGNDTWYGNEMWYGNDS
WYANDTWNSHASWATNDTFDWDAYISDEGNFYFLEGSNDALLCGNSSDAGHCPEGYECIK
TGRNPNYGYTSYDTFSWAFLALFRLMTQDYWENLFQLTLRAAGKTYMIFFVVIIFLGSFY
LINLILAVVAMAYAEQNEATLAEDKEKEEEFQQMLEKFKKHQEELEKAKAAQALEGGEAD
GDPAHGKDCNGSLDTSQGEKGAPRQSSSGDSGISDAMEELEEAHQKCPPWWYKCAHKVLI
WNCCAPWLKFKNIIHLIVMDPFVDLGITICIVLNTLFMAMEHYPMTEHFDNVLTVGNLVF
TGIFTAEMVLKLIAMDPYEYFQQGWNIFDSIIVTLSLVELGLANVQGLSVLRSFRLLRVF
KLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYKECVCKIALDC
NLPRWHMHDFFHSFLIVFRILCGEWIETMWDCMEVAGQAMCLTVFLMVMVIGNLVVLNLF
LALLLSSFSADSLAASDEDGEMNNLQIAIGRIKLGIGFAKAFLLGLLHGKILSPKDIMLS
LGEADGAGEAGEAGETAPEDEKKEPPEEDLKKDNHILNHMGLADGPPSSLELDHLNFINN
PYLTIQVPIASEESDLEMPTEEETDTFSEPEDSKKPPQPLYDGNSSVCSTADYKPPEEDP
EEQAEENPEGEQPEECFTEACVQRWPCLYVDISQGRGKKWWTLRRACFKIVEHNWFETFI
VFMILLSSGALAFEDIYIEQRRVIRTILEYADKVFTYIFIMEMLLKWVAYGFKVYFTNAW
CWLDFLIVDVSIISLVANWLGYSELGPIKSLRTLRALRPLRALSRFEGMRVVVNALLGAI
PSIMNVLLVCLIFWLIFSIMGVNLFAGKFYYCINTTTSERFDISEVNNKSECESLMHTGQ
VRWLNVKVNYDNVGLGYLSLLQVATFKGWMDIMYAAVDSREKEEQPQYEVNLYMYLYFVI
FIIFGSFFTLNLFIGVIIDNFNQQKKKLGGKDIFMTEEQKKYYNAMKKLGSKKPQKPIPR
PQNKIQGMVYDLVTKQAFDITIMILICLNMVTMMVETDNQSQLKVDILYNINMIFIIIFT
GECVLKMLALRQYYFTVGWNIFDFVVVILSIVGLALSDLIQKYFVSPTLFRVIRLARIGR
VLRLIRGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYSIFGMSNFAYVKKESGIDDMF
NFETFGNSIICLFEITTSAGWDGLLNPILNSGPPDCDPNLENPGTSVKGDCGNPSIGICF
FCSYIIISFLIVVNMYIAIILENFNVATEESSEPLGEDDFEMFYETWEKFDPDATQFIAY
SRLSDFVDTLQEPLRIAKPNKIKLITLDLPMVPGDKIHCLDILFALTKEVLGDSGEMDAL
KQTMEEKFMAANPSKVSYEPITTTLKRKHEEVCAIKIQRAYRRHLLQRSMKQASYMYRHS
HDGSGDDAPEKEGLLANTMSKMYGHENGNSSSPSPEEKGEAGDAGPTMGLMPISPSDTAW
PPAPPPGQTVRPGVKESLV
Sequence of entity 2 (B), FASTA
>6AGF_2 Sodium channel subunit beta-1 (chains B)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAE

Ligands and cofactors

IDNameFormulaCopies
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O62
9Z9(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-enC34 H56 O51
6OU[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-y…C39 H76 N O8 P6

Primary citation

Structure of the human voltage-gated sodium channel Nav1.4 in complex with beta 1. Pan, X., Li, Z., Zhou, Q. et al. Science (2018) 362. DOI 10.1126/science.aau2486 · PubMed

Other PDB entries of the same protein (UniProt P35499 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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