Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Sodium channel protein type 1 subunit alpha

Gene

Scn1a

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. Plays a key role in brain, probably by regulating the moment when neurotransmitters are released in neurons. Involved in sensory perception of mechanical pain: activation in somatosensory neurons induces pain without neurogenic inflammation and produces hypersensitivity to mechanical, but not thermal stimuli.By similarity

Enzyme regulationi

Specifically activated by the H.maculata toxins Hm1a and Hm1b in somatosensory neurons to elicit acute pain and mechanical allodynia.By similarity

GO - Molecular functioni

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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ion channel, Sodium channel, Voltage-gated channel

Keywords - Biological processi

Ion transport, Sodium transport, Transport

Keywords - Ligandi

Sodium

Names & Taxonomyi

Protein namesi
Recommended name:
Sodium channel protein type 1 subunit alpha
Alternative name(s):
Sodium channel protein brain I subunit alpha
Sodium channel protein type I subunit alpha
Voltage-gated sodium channel subunit alpha Nav1.1
Gene namesi
Name:Scn1a
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi69364. Scn1a.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 123CytoplasmicSequence analysisAdd BLAST123
Transmembranei124 – 147Helical; Name=S1 of repeat IAdd BLAST24
Topological domaini148 – 155ExtracellularSequence analysis8
Transmembranei156 – 175Helical; Name=S2 of repeat IAdd BLAST20
Topological domaini176 – 188CytoplasmicSequence analysisAdd BLAST13
Transmembranei189 – 207Helical; Name=S3 of repeat IAdd BLAST19
Topological domaini208 – 213ExtracellularSequence analysis6
Transmembranei214 – 233Helical; Voltage-sensor; Name=S4 of repeat IAdd BLAST20
Topological domaini234 – 249CytoplasmicSequence analysisAdd BLAST16
Transmembranei250 – 273Helical; Name=S5 of repeat IAdd BLAST24
Topological domaini274 – 399ExtracellularSequence analysisAdd BLAST126
Transmembranei400 – 425Helical; Name=S6 of repeat IAdd BLAST26
Topological domaini426 – 762CytoplasmicSequence analysisAdd BLAST337
Transmembranei763 – 787Helical; Name=S1 of repeat IIAdd BLAST25
Topological domaini788 – 798ExtracellularSequence analysisAdd BLAST11
Transmembranei799 – 822Helical; Name=S2 of repeat IIAdd BLAST24
Topological domaini823 – 830CytoplasmicSequence analysis8
Transmembranei831 – 850Helical; Name=S3 of repeat IIAdd BLAST20
Topological domaini851 – 856ExtracellularSequence analysis6
Transmembranei857 – 876Helical; Voltage-sensor; Name=S4 of repeat IIAdd BLAST20
Topological domaini877 – 892CytoplasmicSequence analysisAdd BLAST16
Transmembranei893 – 913Helical; Name=S5 of repeat IIAdd BLAST21
Topological domaini914 – 966ExtracellularSequence analysisAdd BLAST53
Transmembranei967 – 992Helical; Name=S6 of repeat IIAdd BLAST26
Topological domaini993 – 1213CytoplasmicSequence analysisAdd BLAST221
Transmembranei1214 – 1237Helical; Name=S1 of repeat IIIAdd BLAST24
Topological domaini1238 – 1250ExtracellularSequence analysisAdd BLAST13
Transmembranei1251 – 1276Helical; Name=S2 of repeat IIIAdd BLAST26
Topological domaini1277 – 1282CytoplasmicSequence analysis6
Transmembranei1283 – 1304Helical; Name=S3 of repeat IIIAdd BLAST22
Topological domaini1305 – 1308ExtracellularSequence analysis4
Transmembranei1309 – 1330Helical; Voltage-sensor; Name=S4 of repeat IIIAdd BLAST22
Topological domaini1331 – 1349CytoplasmicSequence analysisAdd BLAST19
Transmembranei1350 – 1377Helical; Name=S5 of repeat IIIAdd BLAST28
Topological domaini1378 – 1456ExtracellularSequence analysisAdd BLAST79
Transmembranei1457 – 1483Helical; Name=S6 of repeat IIIAdd BLAST27
Topological domaini1484 – 1536CytoplasmicSequence analysisAdd BLAST53
Transmembranei1537 – 1560Helical; Name=S1 of repeat IVAdd BLAST24
Topological domaini1561 – 1571ExtracellularSequence analysisAdd BLAST11
Transmembranei1572 – 1595Helical; Name=S2 of repeat IVAdd BLAST24
Topological domaini1596 – 1601CytoplasmicSequence analysis6
Transmembranei1602 – 1625Helical; Name=S3 of repeat IVAdd BLAST24
Topological domaini1626 – 1635ExtracellularSequence analysis10
Transmembranei1636 – 1657Helical; Voltage-sensor; Name=S4 of repeat IVAdd BLAST22
Topological domaini1658 – 1672CytoplasmicSequence analysisAdd BLAST15
Transmembranei1673 – 1695Helical; Name=S5 of repeat IVAdd BLAST23
Topological domaini1696 – 1761ExtracellularSequence analysisAdd BLAST66
Transmembranei1762 – 1786Helical; Name=S6 of repeat IVAdd BLAST25
Topological domaini1787 – 2009CytoplasmicSequence analysisAdd BLAST223

GO - Cellular componenti

  • plasma membrane Source: RGD
  • voltage-gated sodium channel complex Source: RGD
  • Z disc Source: BHF-UCL
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL4906.
GuidetoPHARMACOLOGYi578.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000484901 – 2009Sodium channel protein type 1 subunit alphaAdd BLAST2009

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi211N-linked (GlcNAc...)Sequence analysis1
Glycosylationi284N-linked (GlcNAc...)Sequence analysis1
Glycosylationi295N-linked (GlcNAc...)Sequence analysis1
Glycosylationi301N-linked (GlcNAc...)Sequence analysis1
Glycosylationi306N-linked (GlcNAc...)Sequence analysis1
Glycosylationi338N-linked (GlcNAc...)Sequence analysis1
Modified residuei470Phosphoserine1 Publication1
Modified residuei523PhosphoserineCombined sources1
Modified residuei525PhosphoserineCombined sources1
Modified residuei550PhosphoserineCombined sources1
Modified residuei551PhosphoserineCombined sources1 Publication1
Modified residuei607Phosphoserine1 Publication1
Modified residuei730PhosphoserineCombined sources1
Glycosylationi1378N-linked (GlcNAc...)Sequence analysis1
Glycosylationi1392N-linked (GlcNAc...)Sequence analysis1
Glycosylationi1403N-linked (GlcNAc...)Sequence analysis1
Modified residuei1516Phosphoserine; by PKCBy similarity1

Post-translational modificationi

Phosphorylation at Ser-1516 by PKC in a highly conserved cytoplasmic loop slows inactivation of the sodium channel and reduces peak sodium currents.By similarity

Keywords - PTMi

Glycoprotein, Phosphoprotein

Proteomic databases

PaxDbiP04774.
PRIDEiP04774.

PTM databases

iPTMnetiP04774.
PhosphoSitePlusiP04774.
SwissPalmiP04774.

Interactioni

Subunit structurei

The voltage-sensitive sodium channel consists of an ion conducting pore forming alpha-subunit regulated by one or more beta-1 (SCN1B), beta-2 (SCN2B), beta-3 (SCN3B) and/or beta-3 (SCN4B). Beta-1 (SCN1B) and beta-3 (SCN3B) are non-covalently associated with alpha, while beta-2 (SCN2B) is covalently linked by disulfide bonds. Interacts with FGF13; may regulate SCN1A activity. Interacts with SCN1B.By similarity

Protein-protein interaction databases

BioGridi249530. 1 interactor.
STRINGi10116.ENSRNOP00000008026.

Chemistry databases

BindingDBiP04774.

Structurei

3D structure databases

ProteinModelPortaliP04774.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati110 – 454ICuratedAdd BLAST345
Repeati750 – 1022IICuratedAdd BLAST273
Repeati1200 – 1514IIICuratedAdd BLAST315
Repeati1523 – 1821IVCuratedAdd BLAST299
Domaini1915 – 1944IQAdd BLAST30

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1561 – 1571S1-S2 loop of repeat IVBy similarityAdd BLAST11
Regioni1619 – 1636S3b-S4 loop of repeat IVBy similarityAdd BLAST18

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.
The S3b-S4 and S1-S2 loops of repeat IV are targeted by H.maculata toxins Hm1a and Hm1b, leading to inhibit fast inactivation of Nav1.1/SCN1A. Selectivity for H.maculata toxins Hm1a and Hm1b depends on S1-S2 loops of repeat IV.By similarity

Sequence similaritiesi

Contains 1 IQ domain.Curated

Keywords - Domaini

Repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410INF8. Eukaryota.
COG1226. LUCA.
HOGENOMiHOG000231755.
HOVERGENiHBG053100.
InParanoidiP04774.
KOiK04833.
PhylomeDBiP04774.

Family and domain databases

Gene3Di1.20.120.350. 4 hits.
InterProiIPR027359. Channel_four-helix_dom.
IPR005821. Ion_trans_dom.
IPR008051. Na_channel_a1su.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
IPR024583. Na_trans_cytopl.
[Graphical view]
PfamiPF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
PF11933. Na_trans_cytopl. 1 hit.
[Graphical view]
PRINTSiPR00170. NACHANNEL.
PR01664. NACHANNEL1.

Sequencei

Sequence statusi: Complete.

P04774-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEQTVLVPPG PDSFNFFTRE SLAAIERRIA EEKAKNPKPD KKDDDENGPK
60 70 80 90 100
PNSDLEAGKN LPFIYGDIPP EMVSEPLEDL DPYYINKKTF IVLNKGKAIF
110 120 130 140 150
RFSATSALYI LTPFNPLRKI AIKILVHSLF SMLIMCTILT NCVFMTMSNP
160 170 180 190 200
PDWTKNVEYT FTGIYTFESL IKIIARGFCL EDFTFLRDPW NWLDFTVITF
210 220 230 240 250
AYVTEFVDLG NVSALRTFRV LRALKTISVI PGLKTIVGAL IQSVKKLSDV
260 270 280 290 300
MILTVFCLSV FALIGLQLFM GNLRNKCVQW PPTNASLEEH SIEKNVTTDY
310 320 330 340 350
NGTLVNETVF EFDWKSYIQD SRYHYFLEGV LDALLCGNSS DAGQCPEGYM
360 370 380 390 400
CVKAGRNPNY GYTSFDTFSW AFLSLFRLMT QDFWENLYQL TLRAAGKTYM
410 420 430 440 450
IFFVLVIFLG SFYLINLILA VVAMAYEEQN QATLEEAEQK EAEFQQMLEQ
460 470 480 490 500
LKKQQEAAQQ AAAATASEHS REPSAAGRLS DSSSEASKLS SKSAKERRNR
510 520 530 540 550
RKKRKQKEQS GGEEKDDDEF HKSESEDSIR RKGFRFSIEG NRLTYEKRYS
560 570 580 590 600
SPHQSLLSIR GSLFSPRRNS RTSLFSFRGR AKDVGSENDF ADDEHSTFED
610 620 630 640 650
NESRRDSLFV PRRHGERRNS NLSQTSRSSR MLAGLPANGK MHSTVDCNGV
660 670 680 690 700
VSLVGGPSVP TSPVGQLLPE VIIDKPATDD NGTTTETEMR KRRSSSFHVS
710 720 730 740 750
MDFLEDPSQR QRAMSIASIL TNTVEELEES RQKCPPCWYK FSNIFLIWDC
760 770 780 790 800
SPYWLKVKHI VNLVVMDPFV DLAITICIVL NTLFMAMEHY PMTEHFNHVL
810 820 830 840 850
TVGNLVFTGI FTAEMFLKII AMDPYYYFQE GWNIFDGFIV TLSLVELGLA
860 870 880 890 900
NVEGLSVLRS FRLLRVFKLA KSWPTLNMLI KIIGNSVGAL GNLTLVLAII
910 920 930 940 950
VFIFAVVGMQ LFGKSYKDCV CKIATDCKLP RWHMNDFFHS FLIVFRVLCG
960 970 980 990 1000
EWIETMWDCM EVAGQAMCLT VFMMVMVIRN LVVLNLFLAL LLSSFSADNL
1010 1020 1030 1040 1050
AATDDDNEMN NLQIAVDRMH KGVAYVKRKI YEFIQQSFVR KQKILDEIKP
1060 1070 1080 1090 1100
LDDLNNRKDN CTSNHTTEIG KDLDCLKDVN GTTSGIGTGS SVEKYIIDES
1110 1120 1130 1140 1150
DYMSFINNPS LTVTVPIAVG ESDFENLNTE DFSSESDLEE SKEKLNESSS
1160 1170 1180 1190 1200
SSEGSTVDIG APAEEQPVME PEETLEPEAC FTEGCVQRFK CCQISVEEGR
1210 1220 1230 1240 1250
GKQWWNLRRT CFRIVEHNWF ETFIVFMILL SSGALAFEDI YIDQRKTIKT
1260 1270 1280 1290 1300
MLEYADKVFT YIFILEMLLK WVAYGYQTYF TNAWCWLDFL IVDVSLVSLT
1310 1320 1330 1340 1350
ANALGYSELG AIKSLRTLRA LRPLRALSRF EGMRVVVNAL LGAIPSIMNV
1360 1370 1380 1390 1400
LLVCLIFWLI FSIMGVNLFA GKFYHCVNTT TGDTFEITEV NNHSDCLKLI
1410 1420 1430 1440 1450
ERNETARWKN VKVNFDNVGF GYLSLLQVAT FKGWMDIMYA AVDSRNVELQ
1460 1470 1480 1490 1500
PKYEESLYMY LYFVIFIIFG SFFTLNLFIG VIIDNFNQQK KKFGGQDIFM
1510 1520 1530 1540 1550
TEEQKKYYNA MKKLGSKKPQ KPIPRPGNKF QGMVFDFVTR QVFDISIMIL
1560 1570 1580 1590 1600
ICLNMVTMMV ETDDQSDYVT SILSRINLVF IVLFTGECVL KLISLRHYYF
1610 1620 1630 1640 1650
TIGWNIFDFV VVILSIVGMF LAELIEKYFV SPTLFRVIRL ARIGRILRLI
1660 1670 1680 1690 1700
KGAKGIRTLL FALMMSLPAL FNIGLLLFLV MFIYAIFGMS NFAYVKREVG
1710 1720 1730 1740 1750
IDDMFNFETF GNSMICLFQI TTSAGWDGLL APILNSKPPD CDPNKVNPGS
1760 1770 1780 1790 1800
SVKGDCGNPS VGIFFFVSYI IISFLVVVNM YIAVILENFS VATEESAEPL
1810 1820 1830 1840 1850
SEDDFEMFYE VWEKFDPDAT QFMEFEKLSQ FAAALEPPLN LPQPNKLQLI
1860 1870 1880 1890 1900
AMDLPMVSGD RIHCLDILFA FTKRVLGESG EMDALRIQME ERFMASNPSK
1910 1920 1930 1940 1950
VSYQPITTTL KRKQEEVSAV IIQRAYRRHL LKRTVKQASF TYNKNKLKGG
1960 1970 1980 1990 2000
ANLLVKEDMI IDRINENSIT EKTDLTMSTA ACPPSYDRVT KPIVEKHEQE

GKDEKAKGK
Length:2,009
Mass (Da):228,770
Last modified:August 13, 1987 - v1
Checksum:i6808466F6368373B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03638 mRNA. Translation: CAA27286.1.
M22253 mRNA. Translation: AAA79965.1.
PIRiA25019.
RefSeqiNP_110502.1. NM_030875.1.
UniGeneiRn.32079.

Genome annotation databases

GeneIDi81574.
KEGGirno:81574.
UCSCiRGD:69364. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03638 mRNA. Translation: CAA27286.1.
M22253 mRNA. Translation: AAA79965.1.
PIRiA25019.
RefSeqiNP_110502.1. NM_030875.1.
UniGeneiRn.32079.

3D structure databases

ProteinModelPortaliP04774.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi249530. 1 interactor.
STRINGi10116.ENSRNOP00000008026.

Chemistry databases

BindingDBiP04774.
ChEMBLiCHEMBL4906.
GuidetoPHARMACOLOGYi578.

PTM databases

iPTMnetiP04774.
PhosphoSitePlusiP04774.
SwissPalmiP04774.

Proteomic databases

PaxDbiP04774.
PRIDEiP04774.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi81574.
KEGGirno:81574.
UCSCiRGD:69364. rat.

Organism-specific databases

CTDi6323.
RGDi69364. Scn1a.

Phylogenomic databases

eggNOGiENOG410INF8. Eukaryota.
COG1226. LUCA.
HOGENOMiHOG000231755.
HOVERGENiHBG053100.
InParanoidiP04774.
KOiK04833.
PhylomeDBiP04774.

Miscellaneous databases

PROiP04774.

Family and domain databases

Gene3Di1.20.120.350. 4 hits.
InterProiIPR027359. Channel_four-helix_dom.
IPR005821. Ion_trans_dom.
IPR008051. Na_channel_a1su.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
IPR024583. Na_trans_cytopl.
[Graphical view]
PfamiPF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
PF11933. Na_trans_cytopl. 1 hit.
[Graphical view]
PRINTSiPR00170. NACHANNEL.
PR01664. NACHANNEL1.
ProtoNetiSearch...

Entry informationi

Entry nameiSCN1A_RAT
AccessioniPrimary (citable) accession number: P04774
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: November 2, 2016
This is version 144 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.