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O88457 (SCNBA_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 95. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Sodium channel protein type 11 subunit alpha
Alternative name(s):
NaN
Sensory neuron sodium channel 2
Sodium channel protein type XI subunit alpha
Voltage-gated sodium channel subunit alpha Nav1.9
Gene names
Name:Scn11a
Synonyms:Nan, Sns2
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length1765 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

This protein 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 sodium ions may pass in accordance with their electrochemical gradient. It is a tetrodotoxin-resistant sodium channel isoform. Also involved, with the contribution of the receptor tyrosine kinase NTRK2, in rapid BDNF-evoked neuronal depolarization By similarity. Ref.2

Subunit structure

The voltage-resistant sodium channel consists of an ion conducting pore forming alpha-subunit regulated by one or more auxiliary subunits SCN1B, SCN2B and SCN3B.

Subcellular location

Membrane; Multi-pass membrane protein By similarity.

Tissue specificity

Expressed (at protein level) in myenteric sensory neurons. Expressed in small sensory neurons of the dorsal root ganglia (C-fiber neurons) and trigeminal ganglia. Ref.1 Ref.2 Ref.3

Developmental stage

Expressed in dorsal root ganglia at 17 dpc onwards. Ref.3

Induction

Down-regulated after axotomy and up-regulated following hind paw inflammation. Down-regulated in vitro by electrical stimulation and by deprivation of NGF. 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.

Sequence similarities

Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.9/SCN11A subfamily. [View classification]

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 17651765Sodium channel protein type 11 subunit alpha
PRO_0000048512

Regions

Transmembrane127 – 14822Helical; Name=S1 of repeat I; By similarity
Transmembrane158 – 17720Helical; Name=S2 of repeat I; By similarity
Transmembrane190 – 20920Helical; Name=S3 of repeat I; By similarity
Transmembrane217 – 23620Helical; Voltage-sensor; Name=S4 of repeat I; By similarity
Transmembrane253 – 26614Helical; Name=S5 of repeat I; By similarity
Transmembrane372 – 39726Helical; Name=S6 of repeat I; By similarity
Transmembrane568 – 59124Helical; Name=S1 of repeat II; By similarity
Transmembrane603 – 62624Helical; Name=S2 of repeat II; By similarity
Transmembrane635 – 65622Helical; Name=S3 of repeat II; By similarity
Transmembrane663 – 68220Helical; Voltage-sensor; Name=S4 of repeat II; By similarity
Transmembrane698 – 72023Helical; Name=S5 of repeat II; By similarity
Transmembrane773 – 79826Helical; Name=S6 of repeat II; By similarity
Transmembrane1030 – 105223Helical; Name=S1 of repeat III; By similarity
Transmembrane1067 – 109226Helical; Name=S2 of repeat III; By similarity
Transmembrane1099 – 111618Helical; Name=S3 of repeat III; By similarity
Transmembrane1118 – 113922Helical; Voltage-sensor; Name=S4 of repeat III; By similarity
Transmembrane1159 – 118022Helical; Name=S5 of repeat III; By similarity
Transmembrane1262 – 128827Helical; Name=S6 of repeat III; By similarity
Transmembrane1342 – 136524Helical; Name=S1 of repeat IV; By similarity
Transmembrane1377 – 140024Helical; Name=S2 of repeat IV; By similarity
Transmembrane1407 – 143024Helical; Name=S3 of repeat IV; By similarity
Transmembrane1441 – 146323Helical; Voltage-sensor; Name=S4 of repeat IV; By similarity
Transmembrane1479 – 150123Helical; Name=S5 of repeat IV; By similarity
Transmembrane1560 – 158425Helical; Name=S6 of repeat IV; By similarity
Repeat126 – 398273I
Repeat567 – 799233II
Repeat1029 – 1289261III
Repeat1341 – 1585245IV

Amino acid modifications

Glycosylation2141N-linked (GlcNAc...) Potential
Glycosylation3191N-linked (GlcNAc...) Potential
Glycosylation3331N-linked (GlcNAc...) Potential
Glycosylation6601N-linked (GlcNAc...) Potential
Glycosylation7231N-linked (GlcNAc...) Potential
Glycosylation11871N-linked (GlcNAc...) Potential
Glycosylation12021N-linked (GlcNAc...) Potential
Glycosylation12071N-linked (GlcNAc...) Potential
Glycosylation12101N-linked (GlcNAc...) Potential
Glycosylation15471N-linked (GlcNAc...) Potential

Sequences

Sequence LengthMass (Da)Tools
O88457 [UniParc].

Last modified November 1, 1998. Version 1.
Checksum: AE8C67397CC60BD9

FASTA1,765201,845
        10         20         30         40         50         60 
MEERYYPVIF PDERNFRPFT SDSLAAIEKR IAIQKERKKS KDKAAAEPQP RPQLDLKASR 

        70         80         90        100        110        120 
KLPKLYGDIP PELVAKPLED LDPFYKDHKT FMVLNKKRTI YRFSAKRALF ILGPFNPLRS 

       130        140        150        160        170        180 
LMIRISVHSV FSMFIICTVI INCMFMANSM ERSFDNDIPE YVFIGIYILE AVIKILARGF 

       190        200        210        220        230        240 
IVDEFSFLRD PWNWLDFIVI GTAIATCFPG SQVNLSALRT FRVFRALKAI SVISGLKVIV 

       250        260        270        280        290        300 
GALLRSVKKL VDVMVLTLFC LSIFALVGQQ LFMGILNQKC IKHNCGPNPA SNKDCFEKEK 

       310        320        330        340        350        360 
DSEDFIMCGT WLGSRPCPNG STCDKTTLNP DNNYTKFDNF GWSFLAMFRV MTQDSWERLY 

       370        380        390        400        410        420 
RQILRTSGIY FVFFFVVVIF LGSFYLLNLT LAVVTMAYEE QNRNVAAETE AKEKMFQEAQ 

       430        440        450        460        470        480 
QLLREEKEAL VAMGIDRSSL NSLQASSFSP KKRKFFGSKT RKSFFMRGSK TAQASASDSE 

       490        500        510        520        530        540 
DDASKNPQLL EQTKRLSQNL PVDLFDEHVD PLHRQRALSA VSILTITMQE QEKFQEPCFP 

       550        560        570        580        590        600 
CGKNLASKYL VWDCSPQWLC IKKVLRTIMT DPFTELAITI CIIINTVFLA VEHHNMDDNL 

       610        620        630        640        650        660 
KTILKIGNWV FTGIFIAEMC LKIIALDPYH YFRHGWNVFD SIVALLSLAD VLYNTLSDNN 

       670        680        690        700        710        720 
RSFLASLRVL RVFKLAKSWP TLNTLIKIIG HSVGALGNLT VVLTIVVFIF SVVGMRLFGT 

       730        740        750        760        770        780 
KFNKTAYATQ ERPRRRWHMD NFYHSFLVVF RILCGEWIEN MWGCMQDMDG SPLCIIVFVL 

       790        800        810        820        830        840 
IMVIGKLVVL NLFIALLLNS FSNEEKDGSL EGETRKTKVQ LALDRFRRAF SFMLHALQSF 

       850        860        870        880        890        900 
CCKKCRRKNS PKPKETTESF AGENKDSILP DARPWKEYDT DMALYTGQAG APLAPLAEVE 

       910        920        930        940        950        960 
DDVEYCGEGG ALPTSQHSAG VQAGDLPPET KQLTSPDDQG VEMEVFSEED LHLSIQSPRK 

       970        980        990       1000       1010       1020 
KSDAVSMLSE CSTIDLNDIF RNLQKTVSPK KQPDRCFPKG LSCHFLCHKT DKRKSPWVLW 

      1030       1040       1050       1060       1070       1080 
WNIRKTCYQI VKHSWFESFI IFVILLSSGA LIFEDVNLPS RPQVEKLLRC TDNIFTFIFL 

      1090       1100       1110       1120       1130       1140 
LEMILKWVAF GFRRYFTSAW CWLDFLIVVV SVLSLMNLPS LKSFRTLRAL RPLRALSQFE 

      1150       1160       1170       1180       1190       1200 
GMKVVVYALI SAIPAILNVL LVCLIFWLVF CILGVNLFSG KFGRCINGTD INMYLDFTEV 

      1210       1220       1230       1240       1250       1260 
PNRSQCNISN YSWKVPQVNF DNVGNAYLAL LQVATYKGWL EIMNAAVDSR EKDEQPDFEA 

      1270       1280       1290       1300       1310       1320 
NLYAYLYFVV FIIFGSFFTL NLFIGVIIDN FNQQQKKLGG QDIFMTEEQK KYYNAMKKLG 

      1330       1340       1350       1360       1370       1380 
TKKPQKPIPR PLNKCQAFVF DLVTSQVFDV IILGLIVLNM IIMMAESADQ PKDVKKTFDI 

      1390       1400       1410       1420       1430       1440 
LNIAFVVIFT IECLIKVFAL RQHYFTNGWN LFDCVVVVLS IISTLVSRLE DSDISFPPTL 

      1450       1460       1470       1480       1490       1500 
FRVVRLARIG RILRLVRAAR GIRTLLFALM MSLPSLFNIG LLLFLVMFIY AIFGMSWFSK 

      1510       1520       1530       1540       1550       1560 
VKKGSGIDDI FNFETFTGSM LCLFQITTSA GWDTLLNPML EAKEHCNSSS QDSCQQPQIA 

      1570       1580       1590       1600       1610       1620 
VVYFVSYIII SFLIVVNMYI AVILENFNTA TEESEDPLGE DDFEIFYEVW EKFDPEASQF 

      1630       1640       1650       1660       1670       1680 
IQYSALSDFA DALPEPLRVA KPNKFQFLVM DLPMVMGDRL HCMDVLFAFT TRVLGDSSGL 

      1690       1700       1710       1720       1730       1740 
DTMKTMMEEK FMEANPFKKL YEPIVTTTKR KEEEQGAAVI QRAYRKHMEK MVKLRLKDRS 

      1750       1760 
SSSHQVFCNG DLSSLDVAKV KVHND 

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References

[1]"NaN, a novel voltage-gated Na channel, is expressed preferentially in peripheral sensory neurons and down-regulated after axotomy."
Dib-Hajj S.D., Tyrrell L., Black J.A., Waxman S.G.
Proc. Natl. Acad. Sci. U.S.A. 95:8963-8968(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY, INDUCTION.
Strain: Sprague-Dawley.
Tissue: Spinal ganglion.
[2]"Two sodium channels contribute to the TTX-R sodium current in primary sensory neurons."
Tate S.N., Benn S.C., Hick C.A., Trezise D., John V.H., Mannion R.J., Costigan M., Plumpton C., Grose D., Gladwell Z., Kendall G., Dale K., Bountra C., Woolf C.J.
Nat. Neurosci. 1:653-655(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION IN VOLTAGE-EVOKED DEPOLARIZATION, TISSUE SPECIFICITY, INDUCTION.
Strain: Sprague-Dawley.
Tissue: Spinal ganglion.
[3]"Developmental expression of the TTX-resistant voltage-gated sodium channels Nav1.8 (SNS) and Nav1.9 (SNS2) in primary sensory neurons."
Benn S.C., Costigan M., Tate S., Fitzgerald M., Woolf C.J.
J. Neurosci. 21:6077-6085(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
[4]"Na+ channel Nav1.9: in search of a gating mechanism."
Delmas P., Coste B.
Trends Neurosci. 26:55-57(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF059030 mRNA. Translation: AAC40199.1.
AJ237852 mRNA. Translation: CAB41850.1.
PIRT42388.
RefSeqNP_062138.1. NM_019265.2.
UniGeneRn.30023.

3D structure databases

ProteinModelPortalO88457.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING10116.ENSRNOP00000033224.

Chemistry

BindingDBO88457.
GuidetoPHARMACOLOGY586.

PTM databases

PhosphoSiteO88457.

Proteomic databases

PaxDbO88457.
PRIDEO88457.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID29701.
KEGGrno:29701.
UCSCRGD:3630. rat.

Organism-specific databases

CTD11280.
RGD3630. Scn11a.

Phylogenomic databases

eggNOGCOG1226.
HOGENOMHOG000231755.
HOVERGENHBG053100.
InParanoidO88457.
KOK04843.
PhylomeDBO88457.

Gene expression databases

GenevestigatorO88457.

Family and domain databases

Gene3D1.20.120.350. 4 hits.
InterProIPR027359. Channel_four-helix_dom.
IPR005821. Ion_trans_dom.
IPR028821. Na_channel_a11su.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
[Graphical view]
PANTHERPTHR10037:SF22. PTHR10037:SF22. 1 hit.
PfamPF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
[Graphical view]
PRINTSPR00170. NACHANNEL.
ProtoNetSearch...

Other

NextBio610107.
PROO88457.

Entry information

Entry nameSCNBA_RAT
AccessionPrimary (citable) accession number: O88457
Entry history
Integrated into UniProtKB/Swiss-Prot: December 21, 2004
Last sequence update: November 1, 1998
Last modified: June 11, 2014
This is version 95 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