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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
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 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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:107636. Scn9a.

Subcellular locationi

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

  • Note: In neurite terminals.By similarity

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 121121CytoplasmicSequence analysisAdd
BLAST
Transmembranei122 – 14524Helical; Name=S1 of repeat ISequence analysisAdd
BLAST
Topological domaini146 – 1538ExtracellularSequence analysis
Transmembranei154 – 17320Helical; Name=S2 of repeat ISequence analysisAdd
BLAST
Topological domaini174 – 18613CytoplasmicSequence analysisAdd
BLAST
Transmembranei187 – 20519Helical; Name=S3 of repeat ISequence analysisAdd
BLAST
Topological domaini206 – 2116ExtracellularSequence analysis
Transmembranei212 – 23120Helical; Voltage-sensor; Name=S4 of repeat ISequence analysisAdd
BLAST
Topological domaini232 – 24716CytoplasmicSequence analysisAdd
BLAST
Transmembranei248 – 27124Helical; Name=S5 of repeat ISequence analysisAdd
BLAST
Topological domaini272 – 378107ExtracellularSequence analysisAdd
BLAST
Transmembranei379 – 40426Helical; Name=S6 of repeat ISequence analysisAdd
BLAST
Topological domaini405 – 737333CytoplasmicSequence analysisAdd
BLAST
Transmembranei738 – 76225Helical; Name=S1 of repeat IISequence analysisAdd
BLAST
Topological domaini763 – 77311ExtracellularSequence analysisAdd
BLAST
Transmembranei774 – 79724Helical; Name=S2 of repeat IISequence analysisAdd
BLAST
Topological domaini798 – 8058CytoplasmicSequence analysis
Transmembranei806 – 82520Helical; Name=S3 of repeat IISequence analysisAdd
BLAST
Topological domaini826 – 8316ExtracellularSequence analysis
Transmembranei832 – 85120Helical; Voltage-sensor; Name=S4 of repeat IISequence analysisAdd
BLAST
Topological domaini852 – 86716CytoplasmicSequence analysisAdd
BLAST
Transmembranei868 – 88821Helical; Name=S5 of repeat IISequence analysisAdd
BLAST
Topological domaini889 – 94153ExtracellularSequence analysisAdd
BLAST
Transmembranei942 – 96726Helical; Name=S6 of repeat IISequence analysisAdd
BLAST
Topological domaini968 – 1185218CytoplasmicSequence analysisAdd
BLAST
Transmembranei1186 – 120924Helical; Name=S1 of repeat IIISequence analysisAdd
BLAST
Topological domaini1210 – 122213ExtracellularSequence analysisAdd
BLAST
Transmembranei1223 – 124826Helical; Name=S2 of repeat IIISequence analysisAdd
BLAST
Topological domaini1249 – 12546CytoplasmicSequence analysis
Transmembranei1255 – 127622Helical; Name=S3 of repeat IIISequence analysisAdd
BLAST
Topological domaini1277 – 12804ExtracellularSequence analysis
Transmembranei1281 – 130222Helical; Voltage-sensor; Name=S4 of repeat IIISequence analysisAdd
BLAST
Topological domaini1303 – 132119CytoplasmicSequence analysisAdd
BLAST
Transmembranei1322 – 134928Helical; Name=S5 of repeat IIISequence analysisAdd
BLAST
Topological domaini1350 – 142879ExtracellularSequence analysisAdd
BLAST
Transmembranei1429 – 145527Helical; Name=S6 of repeat IIISequence analysisAdd
BLAST
Topological domaini1456 – 150853CytoplasmicSequence analysisAdd
BLAST
Transmembranei1509 – 153224Helical; Name=S1 of repeat IVSequence analysisAdd
BLAST
Topological domaini1533 – 154311ExtracellularSequence analysisAdd
BLAST
Transmembranei1544 – 156724Helical; Name=S2 of repeat IVSequence analysisAdd
BLAST
Topological domaini1568 – 15736CytoplasmicSequence analysis
Transmembranei1574 – 159724Helical; Name=S3 of repeat IVSequence analysisAdd
BLAST
Topological domaini1598 – 160710ExtracellularSequence analysis
Transmembranei1608 – 162922Helical; Voltage-sensor; Name=S4 of repeat IVSequence analysisAdd
BLAST
Topological domaini1630 – 164415CytoplasmicSequence analysisAdd
BLAST
Transmembranei1645 – 166723Helical; Name=S5 of repeat IVSequence analysisAdd
BLAST
Topological domaini1668 – 173366ExtracellularSequence analysisAdd
BLAST
Transmembranei1734 – 175825Helical; Name=S6 of repeat IVSequence analysisAdd
BLAST
Topological domaini1759 – 1984226CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Cell projection, Membrane

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL3414411.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 19841984Sodium channel protein type 9 subunit alphaPRO_0000048503Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1488 – 14881Phosphoserine; by PKCBy similarity

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

Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiQ62205.
PaxDbiQ62205.
PRIDEiQ62205.

PTM databases

iPTMnetiQ62205.
PhosphoSiteiQ62205.

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.By similarity1 Publication

Protein-protein interaction databases

BioGridi203104. 2 interactions.
STRINGi10090.ENSMUSP00000097641.

Structurei

3D structure databases

ProteinModelPortaliQ62205.
SMRiQ62205. Positions 1759-1911.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati112 – 410299ICuratedAdd
BLAST
Repeati725 – 988264IICuratedAdd
BLAST
Repeati1178 – 1486309IIICuratedAdd
BLAST
Repeati1495 – 1793299IVCuratedAdd
BLAST
Domaini1887 – 191630IQAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili402 – 44948Sequence analysisAdd
BLAST
Coiled coili684 – 70825Sequence analysisAdd
BLAST

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.By similarity

Sequence similaritiesi

Contains 1 IQ domain.Curated

Keywords - Domaini

Coiled coil, Repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

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

Family and domain databases

Gene3Di1.20.120.350. 4 hits.
InterProiIPR027359. Channel_four-helix_dom.
IPR005821. Ion_trans_dom.
IPR000048. IQ_motif_EF-hand-BS.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
IPR024583. Na_trans_cytopl.
IPR028803. SCN9A.
[Graphical view]
PANTHERiPTHR10037:SF221. PTHR10037:SF221. 2 hits.
PfamiPF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
PF11933. Na_trans_cytopl. 1 hit.
[Graphical view]
PRINTSiPR00170. NACHANNEL.
SMARTiSM00015. IQ. 1 hit.
[Graphical view]

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.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliQ62205.
SMRiQ62205. Positions 1759-1911.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi203104. 2 interactions.
STRINGi10090.ENSMUSP00000097641.

Chemistry

ChEMBLiCHEMBL3414411.

PTM databases

iPTMnetiQ62205.
PhosphoSiteiQ62205.

Proteomic databases

MaxQBiQ62205.
PaxDbiQ62205.
PRIDEiQ62205.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi6335.
MGIiMGI:107636. Scn9a.
RougeiSearch...

Phylogenomic databases

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

Miscellaneous databases

ChiTaRSiScn9a. mouse.
PROiQ62205.
SOURCEiSearch...

Gene expression databases

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

Family and domain databases

Gene3Di1.20.120.350. 4 hits.
InterProiIPR027359. Channel_four-helix_dom.
IPR005821. Ion_trans_dom.
IPR000048. IQ_motif_EF-hand-BS.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
IPR024583. Na_trans_cytopl.
IPR028803. SCN9A.
[Graphical view]
PANTHERiPTHR10037:SF221. PTHR10037:SF221. 2 hits.
PfamiPF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
PF11933. Na_trans_cytopl. 1 hit.
[Graphical view]
PRINTSiPR00170. NACHANNEL.
SMARTiSM00015. IQ. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSCN9A_MOUSE
AccessioniPrimary (citable) accession number: Q62205
Secondary accession number(s): A2ASI7, Q5DTI0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 23, 2004
Last sequence update: January 9, 2007
Last modified: September 7, 2016
This is version 128 of the entry and version 2 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. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.