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Protein

Sodium channel protein type 9 subunit alpha

Gene

Scn9a

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. It is a tetrodotoxin-sensitive Na+ channel isoform. Plays a role in pain mechanisms, especially in the development of inflammatory pain (By similarity).By similarity

GO - Molecular functioni

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

GO - Biological processi

  • behavioral response to pain Source: Ensembl
  • inflammatory response Source: Ensembl
  • membrane depolarization during action potential Source: GO_Central
  • neuronal action potential Source: RGD
  • post-embryonic development Source: Ensembl
  • response to toxic substance Source: Ensembl
  • rhythmic excitation Source: RGD
  • sodium ion transmembrane transport Source: GOC
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 alpha
Alternative name(s):
Peripheral sodium channel 1
Short name:
PN1
Sodium channel protein type IX subunit alpha
Voltage-gated sodium channel subunit alpha Nav1.7
Gene namesi
Name:Scn9a
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494 Componenti: Chromosome 3

Organism-specific databases

RGDi69368. Scn9a.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei122 – 14524Helical; Name=S1 of repeat ISequence AnalysisAdd
BLAST
Transmembranei154 – 17320Helical; Name=S2 of repeat ISequence AnalysisAdd
BLAST
Transmembranei187 – 20519Helical; Name=S3 of repeat ISequence AnalysisAdd
BLAST
Transmembranei212 – 23120Helical; Voltage-sensor; Name=S4 of repeat ISequence AnalysisAdd
BLAST
Transmembranei248 – 27124Helical; Name=S5 of repeat ISequence AnalysisAdd
BLAST
Transmembranei379 – 40426Helical; Name=S6 of repeat ISequence AnalysisAdd
BLAST
Transmembranei738 – 76225Helical; Name=S1 of repeat IISequence AnalysisAdd
BLAST
Transmembranei774 – 79724Helical; Name=S2 of repeat IISequence AnalysisAdd
BLAST
Transmembranei806 – 82520Helical; Name=S3 of repeat IISequence AnalysisAdd
BLAST
Transmembranei832 – 85120Helical; Voltage-sensor; Name=S4 of repeat IISequence AnalysisAdd
BLAST
Transmembranei868 – 88821Helical; Name=S5 of repeat IISequence AnalysisAdd
BLAST
Transmembranei942 – 96726Helical; Name=S6 of repeat IISequence AnalysisAdd
BLAST
Transmembranei1186 – 120924Helical; Name=S1 of repeat IIISequence AnalysisAdd
BLAST
Transmembranei1223 – 124826Helical; Name=S2 of repeat IIISequence AnalysisAdd
BLAST
Transmembranei1255 – 127622Helical; Name=S3 of repeat IIISequence AnalysisAdd
BLAST
Transmembranei1281 – 130222Helical; Voltage-sensor; Name=S4 of repeat IIISequence AnalysisAdd
BLAST
Transmembranei1322 – 134928Helical; Name=S5 of repeat IIISequence AnalysisAdd
BLAST
Transmembranei1429 – 145527Helical; Name=S6 of repeat IIISequence AnalysisAdd
BLAST
Transmembranei1509 – 153224Helical; Name=S1 of repeat IVSequence AnalysisAdd
BLAST
Transmembranei1544 – 156724Helical; Name=S2 of repeat IVSequence AnalysisAdd
BLAST
Transmembranei1574 – 159724Helical; Name=S3 of repeat IVSequence AnalysisAdd
BLAST
Transmembranei1608 – 162922Helical; Voltage-sensor; Name=S4 of repeat IVSequence AnalysisAdd
BLAST
Transmembranei1645 – 166723Helical; Name=S5 of repeat IVSequence AnalysisAdd
BLAST
Transmembranei1734 – 175825Helical; Name=S6 of repeat IVSequence AnalysisAdd
BLAST

GO - Cellular componenti

  • voltage-gated sodium channel complex Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 19841984Sodium channel protein type 9 subunit alphaPRO_0000048505Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi209 – 2091N-linked (GlcNAc...)Sequence Analysis
Glycosylationi283 – 2831N-linked (GlcNAc...)Sequence Analysis
Glycosylationi1350 – 13501N-linked (GlcNAc...)Sequence Analysis
Glycosylationi1364 – 13641N-linked (GlcNAc...)Sequence Analysis
Glycosylationi1373 – 13731N-linked (GlcNAc...)Sequence Analysis
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 (By similarity).By similarity
Phosphorylation at Ser-1488 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, Ubl conjugation

Proteomic databases

PaxDbiO08562.
PRIDEiO08562.

PTM databases

PhosphoSiteiO08562.

Expressioni

Tissue specificityi

Expressed at high level in the dorsal root ganglion and at much lower levels in the brain, sciatic nerve, nodose ganglia, heart, thyroid and adrenal glands and Schwann cells, but not in the cardiac and skeletal muscles, brain and liver.2 Publications

Gene expression databases

GenevestigatoriO08562.

Interactioni

Subunit structurei

The sodium channel consists of a large polypeptide and 2-3 smaller ones. This sequence represents a large polypeptide. Interacts with NEDD4 and NEDD4L (By similarity).By similarity

Structurei

3D structure databases

ProteinModelPortaliO08562.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati121 – 405285IAdd
BLAST
Repeati737 – 968232IIAdd
BLAST
Repeati1185 – 1456272IIIAdd
BLAST
Repeati1508 – 1759252IVAdd
BLAST
Domaini1887 – 191630IQAdd
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.

Sequence similaritiesi

Contains 1 IQ domain.Curated

Keywords - Domaini

Repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG1226.
GeneTreeiENSGT00760000118827.
HOGENOMiHOG000231755.
HOVERGENiHBG053100.
InParanoidiO08562.
KOiK04841.
OMAiLMNVSQN.
OrthoDBiEOG7DJSK9.
PhylomeDBiO08562.
TreeFamiTF323985.

Family and domain databases

Gene3Di1.20.120.350. 4 hits.
InterProiIPR027359. Channel_four-helix_dom.
IPR024583. DUF3451.
IPR005821. Ion_trans_dom.
IPR000048. IQ_motif_EF-hand-BS.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
IPR028803. SCN9A.
[Graphical view]
PANTHERiPTHR10037:SF28. PTHR10037:SF28. 1 hit.
PfamiPF11933. DUF3451. 1 hit.
PF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
[Graphical view]
PRINTSiPR00170. NACHANNEL.
SMARTiSM00015. IQ. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O08562-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAMLPPPGPQ SFVHFTKQSL ALIEQRISEE KAKEHKDEKK DDEEEGPKPS
60 70 80 90 100
SDLEAGKQLP FIYGDIPPGM VSEPLEDLDP YYADKKTFIV LNKGKAIFRF
110 120 130 140 150
NATPALYMLS PFSPLRRISI KILVHSLFSM LIMCTILTNC IFMTLSNPPE
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 LKHKCFRKEL EENETLESIM NTAESEEELK
310 320 330 340 350
KYFYYLEGSK DALLCGFSTD SGQCPEGYIC VKAGRNPDYG YTSFDTFSWA
360 370 380 390 400
FLALFRLMTQ DYWENLYQQT LRAAGKTYMI FFVVVIFLGS FYLINLILAV
410 420 430 440 450
VAMAYEEQNQ ANIEEAKQKE LEFQQMLDRL KKEQEEAEAI AAAAAEFTSI
460 470 480 490 500
GRSRIMGLSE SSSETSRLSS KSAKERRNRR KKKKQKMSSG EEKGDDEKLS
510 520 530 540 550
KSGSEESIRK KSFHLGVEGH HRTREKRLST 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 KFKKLIYFIV MDPFVDLAIT
760 770 780 790 800
ICIVLNTLFM AMEHHPMTEE FKNVLAVGNL IFTGIFAAEM VLKLIAMDPY
810 820 830 840 850
EYFQVGWNIF DSLIVTLSLI ELFLADVEGL SVLRSFRLLR VFKLAKSWPT
860 870 880 890 900
LNMLIKIIGN SVGALGNLTL VLAIIVFIFA VVGMQLFGKS YKECVCKINV
910 920 930 940 950
DCKLPRWHMN DFFHSFLIVF RVLCGEWIET MWDCMEVAGQ TMCLIVYMMV
960 970 980 990 1000
MVIGNLVVLN LFLALLLSSF SSDNLTAIEE DTDANNLQIA VARIKRGINY
1010 1020 1030 1040 1050
VKQTLREFIL KSFSKKPKGS KDTKRTADPN NKKENYISNR TLAEMSKDHN
1060 1070 1080 1090 1100
FLKEKDRISG YGSSLDKSFM DENDYQSFIH NPSLTVTVPI APGESDLEIM
1110 1120 1130 1140 1150
NTEELSSDSD SDYSKEKRNR SSSSECSTVD NPLPGEEEAE AEPVNADEPE
1160 1170 1180 1190 1200
ACFTDGCVRR FPCCQVNVDS 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
TTDGSRFPTS QVANRSECFA LMNVSGNVRW KNLKVNFDNV GLGYLSLLQV
1410 1420 1430 1440 1450
ATFKGWMDIM YAAVDSVNVN EQPKYEYSLY MYIYFVIFII FGSFFTLNLF
1460 1470 1480 1490 1500
IGVIIDNFNQ QKKKLGGQDI FMTEEQKKYY NAMKKLGSKK PQKPIPRPGN
1510 1520 1530 1540 1550
KFQGCIFDLV TNQAFDITIM VLICLNMVTM MVEKEGQTEY MDYVLHWINM
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
GGEMDSLRSQ MEERFMSANP SKVSYEPITT TLKRKQEEVS ATIIQRAYRR
1910 1920 1930 1940 1950
YRLRQHVKNI SSIYIKDGDR DDDLPNKEDT VFDNVNENSS PEKTDVTAST
1960 1970 1980
ISPPSYDSVT KPDQEKYETD KTEKEDKEKD ESRK
Length:1,984
Mass (Da):226,039
Last modified:July 1, 1997 - v1
Checksum:i386C38B9B5097091
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U79568 mRNA. Translation: AAB50403.1.
AF000368 mRNA. Translation: AAB80701.1.
RefSeqiNP_579823.1. NM_133289.1.
UniGeneiRn.88082.

Genome annotation databases

EnsembliENSRNOT00000065126; ENSRNOP00000059170; ENSRNOG00000006639.
GeneIDi78956.
KEGGirno:78956.
UCSCiRGD:69368. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U79568 mRNA. Translation: AAB50403.1.
AF000368 mRNA. Translation: AAB80701.1.
RefSeqiNP_579823.1. NM_133289.1.
UniGeneiRn.88082.

3D structure databases

ProteinModelPortaliO08562.
ModBaseiSearch...
MobiDBiSearch...

Chemistry

BindingDBiO08562.
ChEMBLiCHEMBL3312.
GuidetoPHARMACOLOGYi584.

PTM databases

PhosphoSiteiO08562.

Proteomic databases

PaxDbiO08562.
PRIDEiO08562.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000065126; ENSRNOP00000059170; ENSRNOG00000006639.
GeneIDi78956.
KEGGirno:78956.
UCSCiRGD:69368. rat.

Organism-specific databases

CTDi6335.
RGDi69368. Scn9a.

Phylogenomic databases

eggNOGiCOG1226.
GeneTreeiENSGT00760000118827.
HOGENOMiHOG000231755.
HOVERGENiHBG053100.
InParanoidiO08562.
KOiK04841.
OMAiLMNVSQN.
OrthoDBiEOG7DJSK9.
PhylomeDBiO08562.
TreeFamiTF323985.

Miscellaneous databases

NextBioi614368.
PROiO08562.

Gene expression databases

GenevestigatoriO08562.

Family and domain databases

Gene3Di1.20.120.350. 4 hits.
InterProiIPR027359. Channel_four-helix_dom.
IPR024583. DUF3451.
IPR005821. Ion_trans_dom.
IPR000048. IQ_motif_EF-hand-BS.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
IPR028803. SCN9A.
[Graphical view]
PANTHERiPTHR10037:SF28. PTHR10037:SF28. 1 hit.
PfamiPF11933. DUF3451. 1 hit.
PF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
[Graphical view]
PRINTSiPR00170. NACHANNEL.
SMARTiSM00015. IQ. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Identification of PN1, a predominant voltage-dependent sodium channel expressed principally in peripheral neurons."
    Toledo-Aral J.J., Moss B.L., He Z.J., Koszowski A.G., Whisenand T., Levinson S.R., Wolf J.J., Silos-Santiago I., Halegoua S., Mandel G.
    Proc. Natl. Acad. Sci. U.S.A. 94:1527-1532(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
  2. Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
    Tissue: Spinal ganglion.
  3. Lubec G., Kang S.U., Lubec S.
    Submitted (SEP-2007) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 527-547, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: Sprague-Dawley.
    Tissue: Brain.

Entry informationi

Entry nameiSCN9A_RAT
AccessioniPrimary (citable) accession number: O08562
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 23, 2004
Last sequence update: July 1, 1997
Last modified: February 4, 2015
This is version 103 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, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.