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Protein

Sodium channel protein type 11 subunit alpha

Gene

Scn11a

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

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).By similarity1 Publication

GO - Molecular functioni

GO - Biological processi

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 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 namesi
Name:Scn11a
Synonyms:Nan, Sns2
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi3630. Scn11a.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 126CytoplasmicSequence analysisAdd BLAST126
Transmembranei127 – 148Helical; Name=S1 of repeat IBy similarityAdd BLAST22
Topological domaini149 – 157ExtracellularSequence analysis9
Transmembranei158 – 177Helical; Name=S2 of repeat IBy similarityAdd BLAST20
Topological domaini178 – 189CytoplasmicSequence analysisAdd BLAST12
Transmembranei190 – 209Helical; Name=S3 of repeat IBy similarityAdd BLAST20
Topological domaini210 – 216ExtracellularSequence analysis7
Transmembranei217 – 236Helical; Voltage-sensor; Name=S4 of repeat IBy similarityAdd BLAST20
Topological domaini237 – 252CytoplasmicSequence analysisAdd BLAST16
Transmembranei253 – 266Helical; Name=S5 of repeat IBy similarityAdd BLAST14
Topological domaini267 – 371ExtracellularSequence analysisAdd BLAST105
Transmembranei372 – 397Helical; Name=S6 of repeat IBy similarityAdd BLAST26
Topological domaini398 – 567CytoplasmicSequence analysisAdd BLAST170
Transmembranei568 – 591Helical; Name=S1 of repeat IIBy similarityAdd BLAST24
Topological domaini592 – 602ExtracellularSequence analysisAdd BLAST11
Transmembranei603 – 626Helical; Name=S2 of repeat IIBy similarityAdd BLAST24
Topological domaini627 – 634CytoplasmicSequence analysis8
Transmembranei635 – 656Helical; Name=S3 of repeat IIBy similarityAdd BLAST22
Topological domaini657 – 662ExtracellularSequence analysis6
Transmembranei663 – 682Helical; Voltage-sensor; Name=S4 of repeat IIBy similarityAdd BLAST20
Topological domaini683 – 697CytoplasmicSequence analysisAdd BLAST15
Transmembranei698 – 720Helical; Name=S5 of repeat IIBy similarityAdd BLAST23
Topological domaini721 – 772ExtracellularSequence analysisAdd BLAST52
Transmembranei773 – 798Helical; Name=S6 of repeat IIBy similarityAdd BLAST26
Topological domaini799 – 1029CytoplasmicSequence analysisAdd BLAST231
Transmembranei1030 – 1052Helical; Name=S1 of repeat IIIBy similarityAdd BLAST23
Topological domaini1053 – 1066ExtracellularSequence analysisAdd BLAST14
Transmembranei1067 – 1092Helical; Name=S2 of repeat IIIBy similarityAdd BLAST26
Topological domaini1093 – 1098CytoplasmicSequence analysis6
Transmembranei1099 – 1116Helical; Name=S3 of repeat IIIBy similarityAdd BLAST18
Topological domaini1117ExtracellularSequence analysis1
Transmembranei1118 – 1139Helical; Voltage-sensor; Name=S4 of repeat IIIBy similarityAdd BLAST22
Topological domaini1140 – 1158CytoplasmicSequence analysisAdd BLAST19
Transmembranei1159 – 1180Helical; Name=S5 of repeat IIIBy similarityAdd BLAST22
Topological domaini1181 – 1261ExtracellularSequence analysisAdd BLAST81
Transmembranei1262 – 1288Helical; Name=S6 of repeat IIIBy similarityAdd BLAST27
Topological domaini1289 – 1341CytoplasmicSequence analysisAdd BLAST53
Transmembranei1342 – 1365Helical; Name=S1 of repeat IVBy similarityAdd BLAST24
Topological domaini1366 – 1376ExtracellularSequence analysisAdd BLAST11
Transmembranei1377 – 1400Helical; Name=S2 of repeat IVBy similarityAdd BLAST24
Topological domaini1401 – 1406CytoplasmicSequence analysis6
Transmembranei1407 – 1430Helical; Name=S3 of repeat IVBy similarityAdd BLAST24
Topological domaini1431 – 1440ExtracellularSequence analysis10
Transmembranei1441 – 1463Helical; Voltage-sensor; Name=S4 of repeat IVBy similarityAdd BLAST23
Topological domaini1464 – 1478CytoplasmicSequence analysisAdd BLAST15
Transmembranei1479 – 1501Helical; Name=S5 of repeat IVBy similarityAdd BLAST23
Topological domaini1502 – 1559ExtracellularSequence analysisAdd BLAST58
Transmembranei1560 – 1584Helical; Name=S6 of repeat IVBy similarityAdd BLAST25
Topological domaini1585 – 1765CytoplasmicSequence analysisAdd BLAST181

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Chemistry databases

GuidetoPHARMACOLOGYi586.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000485121 – 1765Sodium channel protein type 11 subunit alphaAdd BLAST1765

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi214N-linked (GlcNAc...)Sequence analysis1
Glycosylationi319N-linked (GlcNAc...)Sequence analysis1
Glycosylationi333N-linked (GlcNAc...)Sequence analysis1
Glycosylationi660N-linked (GlcNAc...)Sequence analysis1
Glycosylationi723N-linked (GlcNAc...)Sequence analysis1
Glycosylationi1187N-linked (GlcNAc...)Sequence analysis1
Glycosylationi1202N-linked (GlcNAc...)Sequence analysis1
Glycosylationi1207N-linked (GlcNAc...)Sequence analysis1
Glycosylationi1210N-linked (GlcNAc...)Sequence analysis1
Glycosylationi1547N-linked (GlcNAc...)Sequence analysis1

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiO88457.
PRIDEiO88457.

PTM databases

iPTMnetiO88457.
PhosphoSitePlusiO88457.

Expressioni

Tissue specificityi

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

Developmental stagei

Expressed in dorsal root ganglia at 17 dpc onwards.1 Publication

Inductioni

Down-regulated after axotomy and up-regulated following hind paw inflammation. Down-regulated in vitro by electrical stimulation and by deprivation of NGF.2 Publications

Interactioni

Subunit structurei

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.

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000033224.

Structurei

3D structure databases

ProteinModelPortaliO88457.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati115 – 403ICuratedAdd BLAST289
Repeati554 – 820IICuratedAdd BLAST267
Repeati1022 – 1319IIICuratedAdd BLAST298
Repeati1328 – 1619IVCuratedAdd BLAST292

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

Keywords - Domaini

Repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410KCTY. Eukaryota.
COG1226. LUCA.
HOGENOMiHOG000231755.
HOVERGENiHBG053100.
InParanoidiO88457.
KOiK04843.
PhylomeDBiO88457.

Family and domain databases

Gene3Di1.20.120.350. 4 hits.
InterProiIPR027359. Channel_four-helix_dom.
IPR005821. Ion_trans_dom.
IPR028821. Na_channel_a11su.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
[Graphical view]
PANTHERiPTHR10037:SF210. PTHR10037:SF210. 1 hit.
PfamiPF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
[Graphical view]
PRINTSiPR00170. NACHANNEL.

Sequencei

Sequence statusi: Complete.

O88457-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEERYYPVIF PDERNFRPFT SDSLAAIEKR IAIQKERKKS KDKAAAEPQP
60 70 80 90 100
RPQLDLKASR KLPKLYGDIP PELVAKPLED LDPFYKDHKT FMVLNKKRTI
110 120 130 140 150
YRFSAKRALF ILGPFNPLRS LMIRISVHSV FSMFIICTVI INCMFMANSM
160 170 180 190 200
ERSFDNDIPE YVFIGIYILE AVIKILARGF IVDEFSFLRD PWNWLDFIVI
210 220 230 240 250
GTAIATCFPG SQVNLSALRT FRVFRALKAI SVISGLKVIV GALLRSVKKL
260 270 280 290 300
VDVMVLTLFC LSIFALVGQQ LFMGILNQKC IKHNCGPNPA SNKDCFEKEK
310 320 330 340 350
DSEDFIMCGT WLGSRPCPNG STCDKTTLNP DNNYTKFDNF GWSFLAMFRV
360 370 380 390 400
MTQDSWERLY RQILRTSGIY FVFFFVVVIF LGSFYLLNLT LAVVTMAYEE
410 420 430 440 450
QNRNVAAETE AKEKMFQEAQ QLLREEKEAL VAMGIDRSSL NSLQASSFSP
460 470 480 490 500
KKRKFFGSKT RKSFFMRGSK TAQASASDSE DDASKNPQLL EQTKRLSQNL
510 520 530 540 550
PVDLFDEHVD PLHRQRALSA VSILTITMQE QEKFQEPCFP CGKNLASKYL
560 570 580 590 600
VWDCSPQWLC IKKVLRTIMT DPFTELAITI CIIINTVFLA VEHHNMDDNL
610 620 630 640 650
KTILKIGNWV FTGIFIAEMC LKIIALDPYH YFRHGWNVFD SIVALLSLAD
660 670 680 690 700
VLYNTLSDNN RSFLASLRVL RVFKLAKSWP TLNTLIKIIG HSVGALGNLT
710 720 730 740 750
VVLTIVVFIF SVVGMRLFGT KFNKTAYATQ ERPRRRWHMD NFYHSFLVVF
760 770 780 790 800
RILCGEWIEN MWGCMQDMDG SPLCIIVFVL IMVIGKLVVL NLFIALLLNS
810 820 830 840 850
FSNEEKDGSL EGETRKTKVQ LALDRFRRAF SFMLHALQSF CCKKCRRKNS
860 870 880 890 900
PKPKETTESF AGENKDSILP DARPWKEYDT DMALYTGQAG APLAPLAEVE
910 920 930 940 950
DDVEYCGEGG ALPTSQHSAG VQAGDLPPET KQLTSPDDQG VEMEVFSEED
960 970 980 990 1000
LHLSIQSPRK KSDAVSMLSE CSTIDLNDIF RNLQKTVSPK KQPDRCFPKG
1010 1020 1030 1040 1050
LSCHFLCHKT DKRKSPWVLW WNIRKTCYQI VKHSWFESFI IFVILLSSGA
1060 1070 1080 1090 1100
LIFEDVNLPS RPQVEKLLRC TDNIFTFIFL LEMILKWVAF GFRRYFTSAW
1110 1120 1130 1140 1150
CWLDFLIVVV SVLSLMNLPS LKSFRTLRAL RPLRALSQFE GMKVVVYALI
1160 1170 1180 1190 1200
SAIPAILNVL LVCLIFWLVF CILGVNLFSG KFGRCINGTD INMYLDFTEV
1210 1220 1230 1240 1250
PNRSQCNISN YSWKVPQVNF DNVGNAYLAL LQVATYKGWL EIMNAAVDSR
1260 1270 1280 1290 1300
EKDEQPDFEA NLYAYLYFVV FIIFGSFFTL NLFIGVIIDN FNQQQKKLGG
1310 1320 1330 1340 1350
QDIFMTEEQK KYYNAMKKLG TKKPQKPIPR PLNKCQAFVF DLVTSQVFDV
1360 1370 1380 1390 1400
IILGLIVLNM IIMMAESADQ PKDVKKTFDI LNIAFVVIFT IECLIKVFAL
1410 1420 1430 1440 1450
RQHYFTNGWN LFDCVVVVLS IISTLVSRLE DSDISFPPTL FRVVRLARIG
1460 1470 1480 1490 1500
RILRLVRAAR GIRTLLFALM MSLPSLFNIG LLLFLVMFIY AIFGMSWFSK
1510 1520 1530 1540 1550
VKKGSGIDDI FNFETFTGSM LCLFQITTSA GWDTLLNPML EAKEHCNSSS
1560 1570 1580 1590 1600
QDSCQQPQIA VVYFVSYIII SFLIVVNMYI AVILENFNTA TEESEDPLGE
1610 1620 1630 1640 1650
DDFEIFYEVW EKFDPEASQF IQYSALSDFA DALPEPLRVA KPNKFQFLVM
1660 1670 1680 1690 1700
DLPMVMGDRL HCMDVLFAFT TRVLGDSSGL DTMKTMMEEK FMEANPFKKL
1710 1720 1730 1740 1750
YEPIVTTTKR KEEEQGAAVI QRAYRKHMEK MVKLRLKDRS SSSHQVFCNG
1760
DLSSLDVAKV KVHND
Length:1,765
Mass (Da):201,845
Last modified:November 1, 1998 - v1
Checksum:iAE8C67397CC60BD9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF059030 mRNA. Translation: AAC40199.1.
AJ237852 mRNA. Translation: CAB41850.1.
PIRiT42388.
RefSeqiNP_062138.1. NM_019265.2.
UniGeneiRn.30023.

Genome annotation databases

GeneIDi29701.
KEGGirno:29701.
UCSCiRGD:3630. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF059030 mRNA. Translation: AAC40199.1.
AJ237852 mRNA. Translation: CAB41850.1.
PIRiT42388.
RefSeqiNP_062138.1. NM_019265.2.
UniGeneiRn.30023.

3D structure databases

ProteinModelPortaliO88457.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000033224.

Chemistry databases

GuidetoPHARMACOLOGYi586.

PTM databases

iPTMnetiO88457.
PhosphoSitePlusiO88457.

Proteomic databases

PaxDbiO88457.
PRIDEiO88457.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi29701.
KEGGirno:29701.
UCSCiRGD:3630. rat.

Organism-specific databases

CTDi11280.
RGDi3630. Scn11a.

Phylogenomic databases

eggNOGiENOG410KCTY. Eukaryota.
COG1226. LUCA.
HOGENOMiHOG000231755.
HOVERGENiHBG053100.
InParanoidiO88457.
KOiK04843.
PhylomeDBiO88457.

Miscellaneous databases

PROiO88457.

Family and domain databases

Gene3Di1.20.120.350. 4 hits.
InterProiIPR027359. Channel_four-helix_dom.
IPR005821. Ion_trans_dom.
IPR028821. Na_channel_a11su.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
[Graphical view]
PANTHERiPTHR10037:SF210. PTHR10037:SF210. 1 hit.
PfamiPF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
[Graphical view]
PRINTSiPR00170. NACHANNEL.
ProtoNetiSearch...

Entry informationi

Entry nameiSCNBA_RAT
AccessioniPrimary (citable) accession number: O88457
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 21, 2004
Last sequence update: November 1, 1998
Last modified: November 2, 2016
This is version 108 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, Reference proteome

Documents

  1. 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.