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O08562 (SCN9A_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 99. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended 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 names
Name:Scn9a
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length1984 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Subunit structure

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.

Subcellular location

Membrane; Multi-pass membrane protein By similarity. Note: In neurite terminals. Ref.1

Tissue specificity

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. Ref.1 Ref.2

Domain

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.

Post-translational modification

Ubiquitinated by NEDD4L; which may promote its endocytosis. Does not seem to be ubiquitinated by NEDD4 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.

Sequence similarities

Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.7/SCN9A subfamily. [View classification]

Contains 1 IQ domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 19841984Sodium channel protein type 9 subunit alpha
PRO_0000048505

Regions

Transmembrane122 – 14524Helical; Name=S1 of repeat I; Potential
Transmembrane154 – 17320Helical; Name=S2 of repeat I; Potential
Transmembrane187 – 20519Helical; Name=S3 of repeat I; Potential
Transmembrane212 – 23120Helical; Voltage-sensor; Name=S4 of repeat I; Potential
Transmembrane248 – 27124Helical; Name=S5 of repeat I; Potential
Transmembrane379 – 40426Helical; Name=S6 of repeat I; Potential
Transmembrane738 – 76225Helical; Name=S1 of repeat II; Potential
Transmembrane774 – 79724Helical; Name=S2 of repeat II; Potential
Transmembrane806 – 82520Helical; Name=S3 of repeat II; Potential
Transmembrane832 – 85120Helical; Voltage-sensor; Name=S4 of repeat II; Potential
Transmembrane868 – 88821Helical; Name=S5 of repeat II; Potential
Transmembrane942 – 96726Helical; Name=S6 of repeat II; Potential
Transmembrane1186 – 120924Helical; Name=S1 of repeat III; Potential
Transmembrane1223 – 124826Helical; Name=S2 of repeat III; Potential
Transmembrane1255 – 127622Helical; Name=S3 of repeat III; Potential
Transmembrane1281 – 130222Helical; Voltage-sensor; Name=S4 of repeat III; Potential
Transmembrane1322 – 134928Helical; Name=S5 of repeat III; Potential
Transmembrane1429 – 145527Helical; Name=S6 of repeat III; Potential
Transmembrane1509 – 153224Helical; Name=S1 of repeat IV; Potential
Transmembrane1544 – 156724Helical; Name=S2 of repeat IV; Potential
Transmembrane1574 – 159724Helical; Name=S3 of repeat IV; Potential
Transmembrane1608 – 162922Helical; Voltage-sensor; Name=S4 of repeat IV; Potential
Transmembrane1645 – 166723Helical; Name=S5 of repeat IV; Potential
Transmembrane1734 – 175825Helical; Name=S6 of repeat IV; Potential
Repeat121 – 405285I
Repeat737 – 968232II
Repeat1185 – 1456272III
Repeat1508 – 1759252IV
Domain1887 – 191630IQ

Amino acid modifications

Modified residue14881Phosphoserine; by PKC By similarity
Glycosylation2091N-linked (GlcNAc...) Potential
Glycosylation2831N-linked (GlcNAc...) Potential
Glycosylation13501N-linked (GlcNAc...) Potential
Glycosylation13641N-linked (GlcNAc...) Potential
Glycosylation13731N-linked (GlcNAc...) Potential

Sequences

Sequence LengthMass (Da)Tools
O08562 [UniParc].

Last modified July 1, 1997. Version 1.
Checksum: 386C38B9B5097091

FASTA1,984226,039
        10         20         30         40         50         60 
MAMLPPPGPQ SFVHFTKQSL ALIEQRISEE KAKEHKDEKK DDEEEGPKPS SDLEAGKQLP 

        70         80         90        100        110        120 
FIYGDIPPGM VSEPLEDLDP YYADKKTFIV LNKGKAIFRF NATPALYMLS PFSPLRRISI 

       130        140        150        160        170        180 
KILVHSLFSM LIMCTILTNC IFMTLSNPPE WTKNVEYTFT GIYTFESLIK ILARGFCVGE 

       190        200        210        220        230        240 
FTFLRDPWNW LDFVVIVFAY LTEFVNLGNV SALRTFRVLR ALKTISVIPG LKTIVGALIQ 

       250        260        270        280        290        300 
SVKKLSDVMI LTVFCLSVFA LIGLQLFMGN LKHKCFRKEL EENETLESIM NTAESEEELK 

       310        320        330        340        350        360 
KYFYYLEGSK DALLCGFSTD SGQCPEGYIC VKAGRNPDYG YTSFDTFSWA FLALFRLMTQ 

       370        380        390        400        410        420 
DYWENLYQQT LRAAGKTYMI FFVVVIFLGS FYLINLILAV VAMAYEEQNQ ANIEEAKQKE 

       430        440        450        460        470        480 
LEFQQMLDRL KKEQEEAEAI AAAAAEFTSI GRSRIMGLSE SSSETSRLSS KSAKERRNRR 

       490        500        510        520        530        540 
KKKKQKMSSG EEKGDDEKLS KSGSEESIRK KSFHLGVEGH HRTREKRLST PNQSPLSIRG 

       550        560        570        580        590        600 
SLFSARRSSR TSLFSFKGRG RDLGSETEFA DDEHSIFGDN ESRRGSLFVP HRPRERRSSN 

       610        620        630        640        650        660 
ISQASRSPPV LPVNGKMHSA VDCNGVVSLV DGPSALMLPN GQLLPEVIID KATSDDSGTT 

       670        680        690        700        710        720 
NQMRKKRLSS SYFLSEDMLN DPHLRQRAMS RASILTNTVE ELEESRQKCP PWWYRFAHTF 

       730        740        750        760        770        780 
LIWNCSPYWI KFKKLIYFIV MDPFVDLAIT ICIVLNTLFM AMEHHPMTEE FKNVLAVGNL 

       790        800        810        820        830        840 
IFTGIFAAEM VLKLIAMDPY EYFQVGWNIF DSLIVTLSLI ELFLADVEGL SVLRSFRLLR 

       850        860        870        880        890        900 
VFKLAKSWPT LNMLIKIIGN SVGALGNLTL VLAIIVFIFA VVGMQLFGKS YKECVCKINV 

       910        920        930        940        950        960 
DCKLPRWHMN DFFHSFLIVF RVLCGEWIET MWDCMEVAGQ TMCLIVYMMV MVIGNLVVLN 

       970        980        990       1000       1010       1020 
LFLALLLSSF SSDNLTAIEE DTDANNLQIA VARIKRGINY VKQTLREFIL KSFSKKPKGS 

      1030       1040       1050       1060       1070       1080 
KDTKRTADPN NKKENYISNR TLAEMSKDHN FLKEKDRISG YGSSLDKSFM DENDYQSFIH 

      1090       1100       1110       1120       1130       1140 
NPSLTVTVPI APGESDLEIM NTEELSSDSD SDYSKEKRNR SSSSECSTVD NPLPGEEEAE 

      1150       1160       1170       1180       1190       1200 
AEPVNADEPE ACFTDGCVRR FPCCQVNVDS GKGKVWWTIR KTCYRIVEHS WFESFIVLMI 

      1210       1220       1230       1240       1250       1260 
LLSSGALAFE DIYIEKKKTI KIILEYADKI FTYIFILEML LKWVAYGYKT YFTNAWCWLD 

      1270       1280       1290       1300       1310       1320 
FLIVDVSLVT LVANTLGYSD LGPIKSLRTL RALRPLRALS RFEGMRVVVN ALIGAIPSIM 

      1330       1340       1350       1360       1370       1380 
NVLLVCLIFW LIFSIMGVNL FAGKFYECVN TTDGSRFPTS QVANRSECFA LMNVSGNVRW 

      1390       1400       1410       1420       1430       1440 
KNLKVNFDNV GLGYLSLLQV ATFKGWMDIM YAAVDSVNVN EQPKYEYSLY MYIYFVIFII 

      1450       1460       1470       1480       1490       1500 
FGSFFTLNLF IGVIIDNFNQ QKKKLGGQDI FMTEEQKKYY NAMKKLGSKK PQKPIPRPGN 

      1510       1520       1530       1540       1550       1560 
KFQGCIFDLV TNQAFDITIM VLICLNMVTM MVEKEGQTEY MDYVLHWINM VFIILFTGEC 

      1570       1580       1590       1600       1610       1620 
VLKLISLRHY YFTVGWNIFD FVVVILSIVG MFLAEMIEKY FVSPTLFRVI RLARIGRILR 

      1630       1640       1650       1660       1670       1680 
LIKGAKGIRT LLFALMMSLP ALFNIGLLLF LVMFIYAIFG MSNFAYVKKE AGINDMFNFE 

      1690       1700       1710       1720       1730       1740 
TFGNSMICLF QITTSAGWDG LLAPILNSAP PDCDPKKVHP GSSVEGDCGN PSVGIFYFVS 

      1750       1760       1770       1780       1790       1800 
YIIISFLVVV NMYIAVILEN FSVATEESTE PLSEDDFEMF YEVWEKFDPD ATQFIEFCKL 

      1810       1820       1830       1840       1850       1860 
SDFAAALDPP LLIAKPNKVQ LIAMDLPMVS GDRIHCLDIL FAFTKRVLGE GGEMDSLRSQ 

      1870       1880       1890       1900       1910       1920 
MEERFMSANP SKVSYEPITT TLKRKQEEVS ATIIQRAYRR YRLRQHVKNI SSIYIKDGDR 

      1930       1940       1950       1960       1970       1980 
DDDLPNKEDT VFDNVNENSS PEKTDVTAST ISPPSYDSVT KPDQEKYETD KTEKEDKEKD 


ESRK 

« Hide

References

[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]"A novel tetrodotoxin-sensitive, voltage-gated sodium channel expressed in rat and human dorsal root ganglia."
Sangameswaran L., Fish L.M., Koch B.D., Rabert D.K., Delgado S.G., Ilnicka M., Jakeman L.B., Novakovic S., Wong K., Sze P., Tzoumaka E., Stewart G.R., Herman R.C., Chan H., Eglen R.M., Hunter J.C.
J. Biol. Chem. 272:14805-14809(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U79568 mRNA. Translation: AAB50403.1.
AF000368 mRNA. Translation: AAB80701.1.
RefSeqNP_579823.1. NM_133289.1.
UniGeneRn.88082.

3D structure databases

ProteinModelPortalO08562.
ModBaseSearch...
MobiDBSearch...

Chemistry

BindingDBO08562.
ChEMBLCHEMBL3312.
GuidetoPHARMACOLOGY584.

PTM databases

PhosphoSiteO08562.

Proteomic databases

PaxDbO08562.
PRIDEO08562.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000065126; ENSRNOP00000059170; ENSRNOG00000006639.
GeneID78956.
KEGGrno:78956.
UCSCRGD:69368. rat.

Organism-specific databases

CTD6335.
RGD69368. Scn9a.

Phylogenomic databases

eggNOGCOG1226.
GeneTreeENSGT00560000076721.
HOGENOMHOG000231755.
HOVERGENHBG053100.
InParanoidO08562.
KOK04841.
OMALMNVSQN.
OrthoDBEOG7DJSK9.
PhylomeDBO08562.
TreeFamTF323985.

Gene expression databases

GenevestigatorO08562.

Family and domain databases

Gene3D1.20.120.350. 4 hits.
InterProIPR027359. 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]
PANTHERPTHR10037:SF28. PTHR10037:SF28. 1 hit.
PfamPF11933. DUF3451. 1 hit.
PF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
[Graphical view]
PRINTSPR00170. NACHANNEL.
SMARTSM00015. IQ. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio614368.
PROO08562.

Entry information

Entry nameSCN9A_RAT
AccessionPrimary (citable) accession number: O08562
Entry history
Integrated into UniProtKB/Swiss-Prot: November 23, 2004
Last sequence update: July 1, 1997
Last modified: June 11, 2014
This is version 99 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families