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Protein

Sodium channel protein type 3 subunit alpha

Gene

Scn3a

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na+ ions may pass in accordance with their electrochemical gradient.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei1503Important residue that permits the spider RTX-VII toxin to inhibit fast inactivation of the channel1 Publication1
Sitei1506Important residue that permits the spider RTX-VII toxin to inhibit fast inactivation of the channel1 Publication1
Sitei1507Important residue that permits the spider RTX-VII toxin to inhibit fast inactivation of the channel1 Publication1
Sitei1510Key residue that permits the spider beta/delta-theraphotoxin-Pre1a to inhibit fast inactivation of the channel1 Publication1
Sitei1562Important residue that permits the spider RTX-VII toxin to inhibit fast inactivation of the channel1 Publication1

GO - Molecular functioni

  • calmodulin binding Source: RGD
  • sodium ion binding Source: RGD
  • voltage-gated sodium channel activity Source: RGD

GO - Biological processi

  • cellular response to antibiotic Source: RGD
  • membrane depolarization during action potential Source: GO_Central
  • nervous system development Source: RGD
  • neuronal action potential Source: RGD
  • response to pyrethroid Source: RGD
  • response to wounding Source: RGD
  • sensory perception of pain Source: RGD

Keywordsi

Molecular functionIon channel, Sodium channel, Voltage-gated channel
Biological processIon transport, Sodium transport, Transport
LigandSodium

Protein family/group databases

TCDBi1.A.1.10.1. the voltage-gated ion channel (vic) superfamily.

Names & Taxonomyi

Protein namesi
Recommended name:
Sodium channel protein type 3 subunit alpha
Alternative name(s):
Sodium channel protein brain III subunit alpha
Sodium channel protein type III subunit alpha
Voltage-gated sodium channel subtype III
Voltage-gated sodium channel subunit alpha Nav1.3
Gene namesi
Name:Scn3a
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi3635. Scn3a.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 128CytoplasmicCuratedAdd BLAST128
Transmembranei129 – 147Helical; Name=S1 of repeat IBy similarityAdd BLAST19
Topological domaini148 – 154ExtracellularCurated7
Transmembranei155 – 175Helical; Name=S2 of repeat IBy similarityAdd BLAST21
Topological domaini176 – 189CytoplasmicCuratedAdd BLAST14
Transmembranei190 – 207Helical; Name=S3 of repeat IBy similarityAdd BLAST18
Topological domaini208 – 213ExtracellularCurated6
Transmembranei214 – 230Helical; Name=S4 of repeat IBy similarityAdd BLAST17
Topological domaini231 – 249CytoplasmicCuratedAdd BLAST19
Transmembranei250 – 269Helical; Name=S5 of repeat IBy similarityAdd BLAST20
Topological domaini270 – 368ExtracellularCuratedAdd BLAST99
Intramembranei369 – 393Pore-formingBy similarityAdd BLAST25
Topological domaini394 – 400ExtracellularCurated7
Transmembranei401 – 421Helical; Name=S6 of repeat IBy similarityAdd BLAST21
Topological domaini422 – 711CytoplasmicCuratedAdd BLAST290
Transmembranei712 – 730Helical; Name=S1 of repeat IIBy similarityAdd BLAST19
Topological domaini731 – 741ExtracellularCuratedAdd BLAST11
Transmembranei742 – 761Helical; Name=S2 of repeat IIBy similarityAdd BLAST20
Topological domaini762 – 775CytoplasmicCuratedAdd BLAST14
Transmembranei776 – 795Helical; Name=S3 of repeat IIBy similarityAdd BLAST20
Topological domaini796 – 797ExtracellularCurated2
Transmembranei798 – 815Helical; Name=S4 of repeat IIBy similarityAdd BLAST18
Topological domaini816 – 831CytoplasmicCuratedAdd BLAST16
Transmembranei832 – 850Helical; Name=S5 of repeat IIBy similarityAdd BLAST19
Topological domaini851 – 879ExtracellularCuratedAdd BLAST29
Intramembranei880 – 900Pore-formingBy similarityAdd BLAST21
Topological domaini901 – 913ExtracellularCuratedAdd BLAST13
Transmembranei914 – 934Helical; Name=S6 of repeat IIBy similarityAdd BLAST21
Topological domaini935 – 1158CytoplasmicCuratedAdd BLAST224
Transmembranei1159 – 1176Helical; Name=S1 of repeat IIIBy similarityAdd BLAST18
Topological domaini1177 – 1189ExtracellularCuratedAdd BLAST13
Transmembranei1190 – 1208Helical; Name=S2 of repeat IIIBy similarityAdd BLAST19
Topological domaini1209 – 1222CytoplasmicCuratedAdd BLAST14
Transmembranei1223 – 1241Helical; Name=S3 of repeat IIIBy similarityAdd BLAST19
Topological domaini1242 – 1249ExtracellularCurated8
Transmembranei1250 – 1268Helical; Name=S4 of repeat IIIBy similarityAdd BLAST19
Topological domaini1269 – 1285CytoplasmicCuratedAdd BLAST17
Transmembranei1286 – 1305Helical; Name=S5 of repeat IIIBy similarityAdd BLAST20
Topological domaini1306 – 1354ExtracellularCuratedAdd BLAST49
Intramembranei1355 – 1376Pore-formingBy similarityAdd BLAST22
Topological domaini1377 – 1393ExtracellularCuratedAdd BLAST17
Transmembranei1394 – 1415Helical; Name=S6 of repeat IIIBy similarityAdd BLAST22
Topological domaini1416 – 1478CytoplasmicCuratedAdd BLAST63
Transmembranei1479 – 1496Helical; Name=S1 of repeat IVBy similarityAdd BLAST18
Topological domaini1497 – 1507ExtracellularCuratedAdd BLAST11
Transmembranei1508 – 1526Helical; Name=S2 of repeat IVBy similarityAdd BLAST19
Topological domaini1527 – 1538CytoplasmicCuratedAdd BLAST12
Transmembranei1539 – 1556Helical; Name=S3 of repeat IVBy similarityAdd BLAST18
Topological domaini1557 – 1569ExtracellularCuratedAdd BLAST13
Transmembranei1570 – 1586Helical; Name=S4 of repeat IVBy similarityAdd BLAST17
Topological domaini1587 – 1605CytoplasmicCuratedAdd BLAST19
Transmembranei1606 – 1623Helical; Name=S5 of repeat IVBy similarityAdd BLAST18
Topological domaini1624 – 1645ExtracellularCuratedAdd BLAST22
Intramembranei1646 – 1668Pore-formingBy similarityAdd BLAST23
Topological domaini1669 – 1698ExtracellularCuratedAdd BLAST30
Transmembranei1699 – 1721Helical; Name=S6 of repeat IVBy similarityAdd BLAST23
Topological domaini1722 – 1951CytoplasmicCuratedAdd BLAST230

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1503K → P: 6-fold decrease in activity of the spider RTX-VII toxin. 1 Publication1
Mutagenesisi1504Y → E: 2-fold decrease in activity of the spider RTX-VII toxin. 1 Publication1
Mutagenesisi1505M → K: 4.5-fold decrease in activity of the spider RTX-VII toxin. 1 Publication1
Mutagenesisi1506T → I: 10-fold decrease in activity of the spider RTX-VII toxin. 1 Publication1
Mutagenesisi1507L → N: 12-fold decrease in activity of the spider RTX-VII toxin. 1 Publication1
Mutagenesisi1562E → Q: 5.5-fold decrease in activity of the spider RTX-VII toxin. 1 Publication1
Mutagenesisi1562E → R: 20-fold decrease in activity of the spider RTX-VII toxin. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL4966.
GuidetoPHARMACOLOGYi580.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000484941 – 1951Sodium channel protein type 3 subunit alphaAdd BLAST1951

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi211N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi277 ↔ 346By similarity
Glycosylationi290N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi296N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi302N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi307N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi339N-linked (GlcNAc...) asparagineSequence analysis1
Modified residuei484PhosphoserineCombined sources1
Modified residuei485PhosphoserineCombined sources1
Modified residuei486PhosphoserineCombined sources1
Disulfide bondi862Interchain; with SCN2B or SCN4BBy similarity
Disulfide bondi862Interchain; with the conotoxin GVIIJ (when the channel is not linked to SCN2B or SCN4B; the bond to SCN2B or SCN4B protects the channel from the inhibition by toxin)By similarity
Disulfide bondi902 ↔ 911By similarity
Glycosylationi1317N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi1331N-linked (GlcNAc...) asparagineSequence analysis1
Modified residuei1452Phosphoserine; by PKCBy similarity1

Post-translational modificationi

May be ubiquitinated by NEDD4L; which would promote its endocytosis.By similarity
Phosphorylation at Ser-1452 by PKC in a highly conserved cytoplasmic loop slows inactivation of the sodium channel and reduces peak sodium currents.By similarity

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiP08104.
PRIDEiP08104.

PTM databases

iPTMnetiP08104.
PhosphoSitePlusiP08104.
SwissPalmiP08104.

Interactioni

Subunit structurei

Heterooligomer of a large alpha subunit and 2-3 smaller beta subunits. Heterooligomer with SCN2B or SCN4B; disulfide-linked. Interacts with NEDD4L. Interacts with the conotoxin GVIIJ (PubMed:24497506). Interacts with the conotoxin GVIIJ (PubMed:24497506). Interacts with the spider beta/delta-theraphotoxin-Pre1a (PubMed:28428547). Interacts with the spider RTX-VII toxin (AC P0DL75) (PubMed:25784299).By similarity3 Publications

GO - Molecular functioni

  • calmodulin binding Source: RGD

Protein-protein interaction databases

BioGridi269080. 2 interactors.
STRINGi10116.ENSRNOP00000006646.

Chemistry databases

BindingDBiP08104.

Structurei

Secondary structure

11951
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi161 – 174Combined sources14

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1QG9NMR-A156-176[»]
ProteinModelPortaliP08104.
SMRiP08104.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP08104.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati110 – 455ICuratedAdd BLAST346
Repeati693 – 965IICuratedAdd BLAST273
Repeati1139 – 1450IIICuratedAdd BLAST312
Repeati1459 – 1757IVCuratedAdd BLAST299
Domaini1851 – 1880IQAdd BLAST30

Domaini

The sequence contains 4 internal repeats, each with 5 hydrophobic segments (S1, S2, S3, S5, S6) and one positively charged segment (S4). Segments S4 are probably the voltage-sensors and are characterized by a series of positively charged amino acids at every third position.Curated

Sequence similaritiesi

Keywords - Domaini

Repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG2301. Eukaryota.
ENOG410XNP6. LUCA.
HOVERGENiHBG053100.
InParanoidiP08104.
KOiK04836.
PhylomeDBiP08104.

Family and domain databases

InterProiView protein in InterPro
IPR005821. Ion_trans_dom.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
IPR024583. Na_trans_cytopl.
PfamiView protein in Pfam
PF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
PF11933. Na_trans_cytopl. 1 hit.
PRINTSiPR00170. NACHANNEL.

Sequencei

Sequence statusi: Complete.

P08104-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQALLVPPG PESFRLFTRE SLAAIEKRAA EEKAKKPKKE QDIDDENKPK
60 70 80 90 100
PNSDLEAGKN LPFIYGDIPP EMVSEPLEDL DPYYVSKKTF VVLNKGKAIF
110 120 130 140 150
RFSATSALYI LTPLNPVRKI AIKILVHSLF SMLIMCTILT NCVFMTLSNP
160 170 180 190 200
PDWTKNVEYT FTGIYTFESL IKILARGFCL EDFTFLRDPW NWLDFSVIVM
210 220 230 240 250
AYVTEFVDLG NVSALRTFRV LRALKTISVI PGLKTIVGAL IQSVKKLSDV
260 270 280 290 300
MILTVFCLSV FALIGLQLFM GNLRNKCSQW PPSDSAFETN TTSYFNGTMD
310 320 330 340 350
SNGTFVNVTM STFNWKDYIA DDSHFYVLDG QKDPLLCGNG SDAGQCPEGY
360 370 380 390 400
ICVKAGRNPN YGYTSFDTFS WAFLSLFRLM TQDYWENLYQ LTLRAAGKTY
410 420 430 440 450
MIFFVLVIFL GSFYLVNLIL AVVAMAYEEQ NQATLEEAEQ KEAEFQQMLE
460 470 480 490 500
QLKKQQEEAQ AVAAASAASR DFSGIGGLGE LLESSSEASK LSSKSAKEWR
510 520 530 540 550
NRRKKRRQRE HLEGNHRADG DRFPKSESED SVKRRSFLLS LDGNPLTGDK
560 570 580 590 600
KLCSPHQSLL SIRGSLFSPR RNSKTSIFSF RGRAKDVGSE NDFADDEHST
610 620 630 640 650
FEDSESRRDS LFVPHRPGER RNSNGTTTET EVRKRRLSSY QISMEMLEDS
660 670 680 690 700
SGRQRSMSIA SILTNTMEEL EESRQKCPPC WYRFANVFLI WDCCDAWLKV
710 720 730 740 750
KHLVNLIVMD PFVDLAITIC IVLNTLFMAM EHYPMTQQFS SVLTVGNLVF
760 770 780 790 800
TGIFTAEMVL KIIAMDPYYY FQEGWNIFDG IIVSLSLMEL GLANVEGLSV
810 820 830 840 850
LRSFRLLRVF KLAKSWPTLN MLIKIIGNSV GALGNLTLVL AIIVFIFAVV
860 870 880 890 900
GMQLFGKSYK ECVCKINVDC KLPRWHMNDF FHSFLIVFRV LCGEWIETMW
910 920 930 940 950
DCMEVAGQTM CLIVFMLVMV IGNLVVLNLF LALLLSSFSS DNLAATDDDN
960 970 980 990 1000
EMNNLQIAVG RMQKGIDFVK NKIRECFRKA FFRKPKVIEI QEGNKIDSCM
1010 1020 1030 1040 1050
SNNTGIEISK ELNYLKDGNG TTSGVGTGSS VEKYVIDEND YMSFINNPSL
1060 1070 1080 1090 1100
TVTVPIAVGE SDFENLNTEE FSSESELEES KEKLNATSSS EGSTVDVAPP
1110 1120 1130 1140 1150
REGEQAEIEP EEDLKPEACF TEGCIKKFPF CQVSTEEGKG KIWWNLRKTC
1160 1170 1180 1190 1200
YSIVEHNWFE TFIVFMILLS SGALAFEDIY IEQRKTIKTM LEYADKVFTY
1210 1220 1230 1240 1250
IFILEMLLKW VAYGFQTYFT NAWCWLDFLI VDVSLVSLVA NALGYSELGA
1260 1270 1280 1290 1300
IKSLRTLRAL RPLRALSRFE GMRVVVNALV GAIPSIMNVL LVCLIFWLIF
1310 1320 1330 1340 1350
SIMGVNLFAG KFYHCVNTTT GNMFEIKEVN NFSDCQALGK QARWKNVKVN
1360 1370 1380 1390 1400
FDNVGAGYLA LLQVATFKGW MDIMYAAVDS RDVKLQPIYE ENLYMYLYFV
1410 1420 1430 1440 1450
IFIIFGSFFT LNLFIGVIID NFNQQKKKFG GQDIFMTEEQ KKYYNAMKKL
1460 1470 1480 1490 1500
GSKKPQKPIP RPANKFQGMV FDFVTRQVFD ISIMILICLN MVTMMVETDD
1510 1520 1530 1540 1550
QSKYMTLVLS RINLVFIVLF TGEFLLKLIS LRYYYFTIGW NIFDFVVVIL
1560 1570 1580 1590 1600
SIVGMFLAEL IEKYFVSPTL FRVIRLARIG RILRLIKGAK GIRTLLFALM
1610 1620 1630 1640 1650
MSLPALFNIG LLLFLVMFIY AIFGMSNFAY VKKEAGIDDM FNFETFGNSM
1660 1670 1680 1690 1700
ICLFQITTSA GWDGLLAPIL NSAPPDCDPD AIHPGSSVKG DCGNPSVGIF
1710 1720 1730 1740 1750
FFVSYIIISF LVVVNMYIAV ILENFSVATE ESAEPLSEDD FEMFYEVWEK
1760 1770 1780 1790 1800
FDPDATQFIE FCKLSDFAAA LDPPLLIAKP NKVQLIAMDL PMVSGDRIHC
1810 1820 1830 1840 1850
LDILFAFTKR VLGESGEMDA LRIQMEDRFM ASNPSKVSYE PITTTLKRKQ
1860 1870 1880 1890 1900
EEVSAAIIQR NYRCYLLKQR LKNISSKYDK ETIKGRIDLP IKGDMVIDKL
1910 1920 1930 1940 1950
NGNSTPEKTD GSSSTTSPPS YDSVTKPDKE KFEKDKPEKE IKGKEVRENQ

K
Length:1,951
Mass (Da):221,387
Last modified:August 1, 1988 - v1
Checksum:i74E5E851524BD10E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y00766 mRNA. Translation: CAA68735.1.
PIRiS00320.
RefSeqiNP_037251.1. NM_013119.1.
UniGeneiRn.87394.

Genome annotation databases

GeneIDi497770.
KEGGirno:497770.

Similar proteinsi

Entry informationi

Entry nameiSCN3A_RAT
AccessioniPrimary (citable) accession number: P08104
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: August 1, 1988
Last modified: November 22, 2017
This is version 155 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families