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Protein

Sodium channel protein type 9 subunit alpha

Gene

Scn9a

Organism
Mus musculus (Mouse)
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 (PubMed:15123669). It is a tetrodotoxin-sensitive Na+ channel isoform. Plays a role in pain mechanisms, especially in the development of inflammatory pain (PubMed:15314237).By similarity2 Publications

GO - Molecular functioni

GO - Biological processi

  • behavioral response to pain Source: MGI
  • inflammatory response Source: MGI
  • membrane depolarization during action potential Source: GO_Central
  • neuronal action potential Source: GO_Central
  • post-embryonic development Source: MGI
  • response to toxic substance Source: MGI
  • sensory perception of pain Source: UniProtKB
  • sodium ion transmembrane transport Source: UniProtKB

Keywordsi

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

Names & Taxonomyi

Protein namesi
Recommended name:
Sodium channel protein type 9 subunit alphaBy similarity
Alternative name(s):
Peripheral sodium channel 1
Short name:
PN1By similarity
Sodium channel protein type IX subunit alpha
Voltage-gated sodium channel subunit alpha Nav1.7
Gene namesi
Name:Scn9aImported
Synonyms:Kiaa41971 Publication
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:107636. Scn9a.

Subcellular locationi

  • Cell membrane 1 Publication; Multi-pass membrane protein By similarity
  • Cell projection By similarity

  • Note: In neurite terminals.By similarity

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 126CytoplasmicCuratedAdd BLAST126
Transmembranei127 – 145Helical; Name=S1 of repeat IBy similarityAdd BLAST19
Topological domaini146 – 152ExtracellularCurated7
Transmembranei153 – 173Helical; Name=S2 of repeat IBy similarityAdd BLAST21
Topological domaini174 – 187CytoplasmicCuratedAdd BLAST14
Transmembranei188 – 205Helical; Name=S3 of repeat IBy similarityAdd BLAST18
Topological domaini206 – 211ExtracellularCurated6
Transmembranei212 – 228Helical; Name=S4 of repeat IBy similarityAdd BLAST17
Topological domaini229 – 247CytoplasmicCuratedAdd BLAST19
Transmembranei248 – 267Helical; Name=S5 of repeat IBy similarityAdd BLAST20
Topological domaini268 – 346ExtracellularCuratedAdd BLAST79
Intramembranei347 – 371Pore-formingBy similarityAdd BLAST25
Topological domaini372 – 378ExtracellularCurated7
Transmembranei379 – 399Helical; Name=S6 of repeat IBy similarityAdd BLAST21
Topological domaini400 – 743CytoplasmicCuratedAdd BLAST344
Transmembranei744 – 762Helical; Name=S1 of repeat IIBy similarityAdd BLAST19
Topological domaini763 – 773ExtracellularCuratedAdd BLAST11
Transmembranei774 – 793Helical; Name=S2 of repeat IIBy similarityAdd BLAST20
Topological domaini794 – 807CytoplasmicCuratedAdd BLAST14
Transmembranei808 – 827Helical; Name=S3 of repeat IIBy similarityAdd BLAST20
Topological domaini828 – 829ExtracellularCurated2
Transmembranei830 – 847Helical; Name=S4 of repeat IIBy similarityAdd BLAST18
Topological domaini848 – 863CytoplasmicCuratedAdd BLAST16
Transmembranei864 – 882Helical; Name=S5 of repeat IIBy similarityAdd BLAST19
Topological domaini883 – 911ExtracellularCuratedAdd BLAST29
Intramembranei912 – 932Pore-formingBy similarityAdd BLAST21
Topological domaini933 – 945ExtracellularCuratedAdd BLAST13
Transmembranei946 – 966Helical; Name=S6 of repeat IIBy similarityAdd BLAST21
Topological domaini967 – 1191CytoplasmicCuratedAdd BLAST225
Transmembranei1192 – 1209Helical; Name=S1 of repeat IIIBy similarityAdd BLAST18
Topological domaini1210 – 1222ExtracellularCuratedAdd BLAST13
Transmembranei1223 – 1241Helical; Name=S2 of repeat IIIBy similarityAdd BLAST19
Topological domaini1242 – 1255CytoplasmicCuratedAdd BLAST14
Transmembranei1256 – 1274Helical; Name=S3 of repeat IIIBy similarityAdd BLAST19
Topological domaini1275 – 1282ExtracellularCurated8
Transmembranei1283 – 1301Helical; Name=S4 of repeat IIIBy similarityAdd BLAST19
Topological domaini1302 – 1318CytoplasmicCuratedAdd BLAST17
Transmembranei1319 – 1338Helical; Name=S5 of repeat IIIBy similarityAdd BLAST20
Topological domaini1339 – 1390ExtracellularCuratedAdd BLAST52
Intramembranei1391 – 1412Pore-formingBy similarityAdd BLAST22
Topological domaini1413 – 1429ExtracellularCuratedAdd BLAST17
Transmembranei1430 – 1451Helical; Name=S6 of repeat IIIBy similarityAdd BLAST22
Topological domaini1452 – 1514CytoplasmicCuratedAdd BLAST63
Transmembranei1515 – 1532Helical; Name=S1 of repeat IVBy similarityAdd BLAST18
Topological domaini1533 – 1543ExtracellularCuratedAdd BLAST11
Transmembranei1544 – 1562Helical; Name=S2 of repeat IVBy similarityAdd BLAST19
Topological domaini1563 – 1574CytoplasmicCuratedAdd BLAST12
Transmembranei1575 – 1592Helical; Name=S3 of repeat IVBy similarityAdd BLAST18
Topological domaini1593 – 1605ExtracellularCuratedAdd BLAST13
Transmembranei1606 – 1622Helical; Name=S4 of repeat IVBy similarityAdd BLAST17
Topological domaini1623 – 1641CytoplasmicCuratedAdd BLAST19
Transmembranei1642 – 1659Helical; Name=S5 of repeat IVBy similarityAdd BLAST18
Topological domaini1660 – 1681ExtracellularCuratedAdd BLAST22
Intramembranei1682 – 1704Pore-formingBy similarityAdd BLAST23
Topological domaini1705 – 1734ExtracellularCuratedAdd BLAST30
Transmembranei1735 – 1757Helical; Name=S6 of repeat IVBy similarityAdd BLAST23
Topological domaini1758 – 1984CytoplasmicCuratedAdd BLAST227

GO - Cellular componenti

Keywords - Cellular componenti

Cell membrane, Cell projection, Membrane

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL3414411.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000485031 – 1984Sodium channel protein type 9 subunit alphaAdd BLAST1984

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi275 ↔ 324By similarity
Disulfide bondi894Interchain; with SCN2B or SCN4BBy similarity
Disulfide bondi894Interchain; 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 bondi934 ↔ 943By similarity
Modified residuei1488Phosphoserine; by PKCBy similarity1

Post-translational modificationi

Ubiquitinated by NEDD4L; which may promote its endocytosis. Does not seem to be ubiquitinated by NEDD4.1 Publication
Phosphorylation at Ser-1488 by PKC in a highly conserved cytoplasmic loop increases peak sodium currents.By similarity

Keywords - PTMi

Disulfide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiQ62205.
PaxDbiQ62205.
PRIDEiQ62205.

PTM databases

iPTMnetiQ62205.
PhosphoSitePlusiQ62205.

Expressioni

Gene expression databases

BgeeiENSMUSG00000075316.
CleanExiMM_SCN9A.
ExpressionAtlasiQ62205. baseline and differential.
GenevisibleiQ62205. MM.

Interactioni

Subunit structurei

The sodium channel complex consists of a large, channel-forming alpha subunit and 2-3 smaller, ancillary beta subunits (By similarity). Interacts with NEDD4 and NEDD4L. Interacts with the conotoxin GVIIJ (By similarity).By similarity1 Publication

Protein-protein interaction databases

BioGridi203104. 2 interactors.
STRINGi10090.ENSMUSP00000097641.

Chemistry databases

BindingDBiQ62205.

Structurei

3D structure databases

ProteinModelPortaliQ62205.
SMRiQ62205.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati112 – 410ICuratedAdd BLAST299
Repeati725 – 988IICuratedAdd BLAST264
Repeati1178 – 1486IIICuratedAdd BLAST309
Repeati1495 – 1793IVCuratedAdd BLAST299
Domaini1887 – 1916IQAdd BLAST30

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili402 – 449Sequence analysisAdd BLAST48
Coiled coili684 – 708Sequence analysisAdd BLAST25

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

Coiled coil, Repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG2301. Eukaryota.
ENOG410XNP6. LUCA.
GeneTreeiENSGT00830000128242.
HOGENOMiHOG000231755.
HOVERGENiHBG053100.
InParanoidiQ62205.
KOiK04841.
OMAiRQKCPPW.
OrthoDBiEOG091G00FK.
PhylomeDBiQ62205.
TreeFamiTF323985.

Family and domain databases

InterProiView protein in InterPro
IPR005821. Ion_trans_dom.
IPR000048. IQ_motif_EF-hand-BS.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
IPR024583. Na_trans_cytopl.
IPR028803. SCN9A.
PANTHERiPTHR10037:SF235. PTHR10037:SF235. 1 hit.
PfamiView protein in Pfam
PF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
PF11933. Na_trans_cytopl. 1 hit.
PRINTSiPR00170. NACHANNEL.
SMARTiView protein in SMART
SM00015. IQ. 1 hit.

Sequencei

Sequence statusi: Complete.

Q62205-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAMLPPPGPQ SFVHFTKQSL ALIEQRISEE KAKGHKDEKK DDEEEGPKPS
60 70 80 90 100
SDLEAGKQLP FIYGDIPPGM VSEPLEDLDP YYADKKTFIV LNKGKAIFRF
110 120 130 140 150
NATPALYMLS PFSPLRRISI KILVHSLFSM LIMCTILTNC IFMTMSNPPD
160 170 180 190 200
WTKNVEYTFT GIYTFESLIK ILARGFCVGE FTFLRDPWNW LDFVVIVFAY
210 220 230 240 250
LTEFVNLGNV SALRTFRVLR ALKTISVIPG LKTIVGALIQ SVKKLSDVMI
260 270 280 290 300
LTVFCLSVFA LIGLQLFMGN LKHKCFRKDL EQNETLESIM STAESEEELK
310 320 330 340 350
RYFYYLEGSK DALLCGFSTD SGQCPEGYEC VTAGRNPDYG YTSFDTFGWA
360 370 380 390 400
FLALFRLMTQ DYWENLYQQT LRAAGKTYMI FFVVVIFLGS FYLINLILAV
410 420 430 440 450
VAMAYEEQNQ ANIEEAKQKE LEFQQMLDRL KKEQEEAEAI AAAAAEYTSL
460 470 480 490 500
GRSRIMGLSE SSSETSRLSS KSAKERRNRR KKKKQKLSSG EEKGDDEKLS
510 520 530 540 550
KSGSEESIRK KSFHLGVEGH HRAREKRLST PNQSPLSIRG SLFSARRSSR
560 570 580 590 600
TSLFSFKGRG RDLGSETEFA DDEHSIFGDN ESRRGSLFVP HRPRERRSSN
610 620 630 640 650
ISQASRSPPV LPVNGKMHSA VDCNGVVSLV DGPSALMLPN GQLLPEVIID
660 670 680 690 700
KATSDDSGTT NQMRKKRLSS SYFLSEDMLN DPHLRQRAMS RASILTNTVE
710 720 730 740 750
ELEESRQKCP PWWYRFAHTF LIWNCSPYWI KFKKFIYFIV MDPFVDLAIT
760 770 780 790 800
ICIVLNTLFM AMEHHPMTDE FKNVLAVGNL VFTGIFAAEM VLKLIAMDPY
810 820 830 840 850
EYFQVGWNIF DSLIVTLSLV ELFLADVEGL SVLRSFRLLR VFKLAKSWPT
860 870 880 890 900
LNMLIKIIGN SVGALGNLTL VLAIIVFIFA VVGMQLFGKS YKECVCKINE
910 920 930 940 950
NCKLPRWHMN DFFHSFLIVF RVLCGEWIET MWDCMEVAGQ TMCLIVYMMV
960 970 980 990 1000
MVIGNLVVLN LFLALLLSSF SSDNLTAIEE DTDANNLQIA VARIKRGINY
1010 1020 1030 1040 1050
VKQTLREFIL KSFSKKPKGS KDTKRTADPN NKRENYISNR TLAEISKDHN
1060 1070 1080 1090 1100
FLKEKDKISG FSSSLDKSFM DENDYQSFIH NPSLTVTVPI APGESDLENM
1110 1120 1130 1140 1150
NTEELSSDSD SDYSKERRNR SSSSECSTVD NPLPGEEEAE AEPINADEPE
1160 1170 1180 1190 1200
ACFTDGCVRR FPCCQVNIDS GKGKVWWTIR KTCYRIVEHS WFESFIVLMI
1210 1220 1230 1240 1250
LLSSGALAFE DIYIEKKKTI KIILEYADKI FTYIFILEML LKWVAYGYKT
1260 1270 1280 1290 1300
YFTNAWCWLD FLIVDVSLVT LVANTLGYSD LGPIKSLRTL RALRPLRALS
1310 1320 1330 1340 1350
RFEGMRVVVN ALIGAIPSIM NVLLVCLIFW LIFSIMGVNL FAGKFYECVN
1360 1370 1380 1390 1400
TTDGSRFSVS QVANRSECFA LMNVSGNVRW KNLKVNFDNV GLGYLSLLQV
1410 1420 1430 1440 1450
ATFKGWMDIM YAAVDSVNVN AQPIYEYNLY MYIYFVIFII FGSFFTLNLF
1460 1470 1480 1490 1500
IGVIIDNFNQ QKKKLGGQDI FMTEEQKKYY NAMKKLGSKK PQKPIPRPGN
1510 1520 1530 1540 1550
KFQGCIFDLV TNQAFDITIM VLICLNMVTM MVEKEGQTDY MSFVLYWINV
1560 1570 1580 1590 1600
VFIILFTGEC VLKLISLRHY YFTVGWNIFD FVVVILSIVG MFLAEMIEKY
1610 1620 1630 1640 1650
FVSPTLFRVI RLARIGRILR LIKGAKGIRT LLFALMMSLP ALFNIGLLLF
1660 1670 1680 1690 1700
LVMFIYAIFG MSNFAYVKKE AGINDMFNFE TFGNSMICLF QITTSAGWDG
1710 1720 1730 1740 1750
LLAPILNSAP PDCDPKKVHP GSSVEGDCGN PSVGIFYFVS YIIISFLVVV
1760 1770 1780 1790 1800
NMYIAVILEN FSVATEESTE PLSEDDFEMF YEVWEKFDPD ATQFIEFCKL
1810 1820 1830 1840 1850
SDFAAALDPP LLIAKPNKVQ LIAMDLPMVS GDRIHCLDIL FAFTKRVLGE
1860 1870 1880 1890 1900
SGEMDSLRSQ MEERFMSANP SKVSYEPITT TLKRKQEDVS ATIIQRAYRR
1910 1920 1930 1940 1950
YRLRQNVKNI SSIYIKDGDR DDDLPNKEDI VFDNVNENSS PEKTDATAST
1960 1970 1980
ISPPSYDSVT KPDQEKYETD KTEKEDKEKD ESRK
Length:1,984
Mass (Da):225,813
Last modified:January 9, 2007 - v2
Checksum:i51A8DBA38EC7EF38
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL928623, AL928726 Genomic DNA. Translation: CAM19365.1.
AL928726, AL928623 Genomic DNA. Translation: CAM23210.1.
L42338 mRNA. Translation: AAA67106.1.
AK220540 mRNA. Translation: BAD90315.1.
CCDSiCCDS71063.1.
RefSeqiNP_001277603.1. NM_001290674.1.
UniGeneiMm.440889.

Genome annotation databases

EnsembliENSMUST00000100064; ENSMUSP00000097642; ENSMUSG00000075316.
ENSMUST00000164384; ENSMUSP00000126528; ENSMUSG00000075316.
GeneIDi20274.
KEGGimmu:20274.
UCSCiuc008jxe.4. mouse.

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.

Entry informationi

Entry nameiSCN9A_MOUSE
AccessioniPrimary (citable) accession number: Q62205
Secondary accession number(s): A2ASI7, Q5DTI0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 23, 2004
Last sequence update: January 9, 2007
Last modified: July 5, 2017
This is version 136 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families