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Protein

Sodium channel protein type 11 subunit alpha

Gene

Scn11a

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript 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 similarity

GO - Molecular functioni

  • voltage-gated sodium channel activity Source: MGI

GO - Biological processi

  • membrane depolarization during action potential Source: GO_Central
  • neuronal action potential Source: GO_Central
  • regulation of sensory perception of pain Source: UniProtKB
  • sodium ion transport Source: MGI
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, Nat, Sns2
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 9

Organism-specific databases

MGIiMGI:1345149. 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 – 159ExtracellularSequence analysisAdd BLAST11
Transmembranei160 – 179Helical; Name=S2 of repeat IBy similarityAdd BLAST20
Topological domaini180 – 191CytoplasmicSequence analysisAdd BLAST12
Transmembranei192 – 211Helical; Name=S3 of repeat IBy similarityAdd BLAST20
Topological domaini212 – 219ExtracellularSequence analysis8
Transmembranei220 – 239Helical; Voltage-sensor; Name=S4 of repeat IBy similarityAdd BLAST20
Topological domaini240 – 255CytoplasmicSequence analysisAdd BLAST16
Transmembranei256 – 269Helical; Name=S5 of repeat IBy similarityAdd BLAST14
Topological domaini270 – 374ExtracellularSequence analysisAdd BLAST105
Transmembranei375 – 400Helical; Name=S6 of repeat IBy similarityAdd BLAST26
Topological domaini401 – 570CytoplasmicSequence analysisAdd BLAST170
Transmembranei571 – 594Helical; Name=S1 of repeat IIBy similarityAdd BLAST24
Topological domaini595 – 605ExtracellularSequence analysisAdd BLAST11
Transmembranei606 – 629Helical; Name=S2 of repeat IIBy similarityAdd BLAST24
Topological domaini630 – 637CytoplasmicSequence analysis8
Transmembranei638 – 659Helical; Name=S3 of repeat IIBy similarityAdd BLAST22
Topological domaini660 – 664ExtracellularSequence analysis5
Transmembranei665 – 684Helical; Voltage-sensor; Name=S4 of repeat IIBy similarityAdd BLAST20
Topological domaini685 – 699CytoplasmicSequence analysisAdd BLAST15
Transmembranei700 – 722Helical; Name=S5 of repeat IIBy similarityAdd BLAST23
Topological domaini723 – 773ExtracellularSequence analysisAdd BLAST51
Transmembranei774 – 799Helical; Name=S6 of repeat IIBy similarityAdd BLAST26
Topological domaini800 – 1030CytoplasmicSequence analysisAdd BLAST231
Transmembranei1031 – 1053Helical; Name=S1 of repeat IIIBy similarityAdd BLAST23
Topological domaini1054 – 1067ExtracellularSequence analysisAdd BLAST14
Transmembranei1068 – 1093Helical; Name=S2 of repeat IIIBy similarityAdd BLAST26
Topological domaini1094 – 1099CytoplasmicSequence analysis6
Transmembranei1100 – 1117Helical; Name=S3 of repeat IIIBy similarityAdd BLAST18
Topological domaini1118ExtracellularSequence analysis1
Transmembranei1119 – 1140Helical; Voltage-sensor; Name=S4 of repeat IIIBy similarityAdd BLAST22
Topological domaini1141 – 1159CytoplasmicSequence analysisAdd BLAST19
Transmembranei1160 – 1181Helical; Name=S5 of repeat IIIBy similarityAdd BLAST22
Topological domaini1182 – 1262ExtracellularSequence analysisAdd BLAST81
Transmembranei1263 – 1289Helical; Name=S6 of repeat IIIBy similarityAdd BLAST27
Topological domaini1290 – 1342CytoplasmicSequence analysisAdd BLAST53
Transmembranei1343 – 1366Helical; Name=S1 of repeat IVBy similarityAdd BLAST24
Topological domaini1367 – 1377ExtracellularSequence analysisAdd BLAST11
Transmembranei1378 – 1401Helical; Name=S2 of repeat IVBy similarityAdd BLAST24
Topological domaini1402 – 1407CytoplasmicSequence analysis6
Transmembranei1408 – 1431Helical; Name=S3 of repeat IVBy similarityAdd BLAST24
Topological domaini1432 – 1440ExtracellularSequence analysis9
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

  • axon Source: MGI
  • C-fiber Source: MGI
  • extracellular exosome Source: MGI
  • plasma membrane Source: MGI
  • voltage-gated sodium channel complex Source: InterPro
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000485111 – 1765Sodium channel protein type 11 subunit alphaAdd BLAST1765

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi149N-linked (GlcNAc...)Sequence analysis1
Glycosylationi217N-linked (GlcNAc...)Sequence analysis1
Glycosylationi303N-linked (GlcNAc...)Sequence analysis1
Glycosylationi327N-linked (GlcNAc...)Sequence analysis1
Glycosylationi336N-linked (GlcNAc...)Sequence analysis1
Glycosylationi662N-linked (GlcNAc...)Sequence analysis1
Glycosylationi725N-linked (GlcNAc...)Sequence analysis1
Glycosylationi1188N-linked (GlcNAc...)Sequence analysis1
Glycosylationi1197N-linked (GlcNAc...)Sequence analysis1
Glycosylationi1203N-linked (GlcNAc...)Sequence analysis1
Glycosylationi1211N-linked (GlcNAc...)Sequence analysis1

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiQ9R053.
PRIDEiQ9R053.

PTM databases

iPTMnetiQ9R053.
PhosphoSitePlusiQ9R053.

Expressioni

Tissue specificityi

Expressed in the dorsal root ganglia (C-fiber neurons), spinal cord, trigeminal ganglia, testis, ovary, uterus and small intestine.1 Publication

Developmental stagei

Expressed in embryo at 15 dpc onwards.1 Publication

Gene expression databases

BgeeiENSMUSG00000034115.
CleanExiMM_SCN11A.
GenevisibleiQ9R053. MM.

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

BioGridi204861. 1 interactor.
STRINGi10090.ENSMUSP00000065466.

Structurei

3D structure databases

ProteinModelPortaliQ9R053.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati115 – 406ICuratedAdd BLAST292
Repeati557 – 821IICuratedAdd BLAST265
Repeati1023 – 1320IIICuratedAdd BLAST298
Repeati1329 – 1619IVCuratedAdd BLAST291

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

eggNOGiKOG2301. Eukaryota.
ENOG410XNP6. LUCA.
GeneTreeiENSGT00830000128242.
HOGENOMiHOG000231755.
HOVERGENiHBG053100.
InParanoidiQ9R053.
KOiK04843.
OMAiLENFNTA.
OrthoDBiEOG091G00FK.
TreeFamiTF323985.

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.

Q9R053-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEERYYPVIF PDERNFRPFT FDSLAAIEKR ITIQKEKKKS KDKAATEPQP
60 70 80 90 100
RPQLDLKASR KLPKLYGDVP PDLIAKPLED LDPFYKDHKT FMVLNKKRTI
110 120 130 140 150
YRFSAKRALF ILGPFNPIRS FMIRISVHSV FSMFIICTVI INCMFMANNS
160 170 180 190 200
SVDSRPSSNI PEYVFIGIYV LEAVIKILAR GFIVDEFSYL RDPWNWLDFI
210 220 230 240 250
VIGTAIAPCF LGNKVNNLST LRTFRVLRAL KAISVISGLK VIVGALLRSV
260 270 280 290 300
KKLVDVMVLT LFCLSIFALV GQQLFMGILS QKCIKDDCGP NAFSNKDCFV
310 320 330 340 350
KENDSEDFIM CGNWLGRRSC PDGSTCNKTT FNPDYNYTNF DSFGWSFLAM
360 370 380 390 400
FRVMTQDSWE KLYRQILRTS GIYFVFFFVV VIFLGSFYLL NLTLAVVTMA
410 420 430 440 450
YEEQNRNVAA ETEAKEKMFQ EAQQLLREEK EALVAMGIDR TSLNSLQASS
460 470 480 490 500
FSPKKRKFFG SKTRKSFFMR GSKTARASAS DSEDDASKNP QLLEQTKRLS
510 520 530 540 550
QNLPVELFDE HVDPLHRQRA LSAVSILTIT MQEQEKSQEP CFPCGKNLAS
560 570 580 590 600
KYLVWECSPP WLCIKKVLQT IMTDPFTELA ITICIIVNTV FLAMEHHNMD
610 620 630 640 650
NSLKDILKIG NWVFTGIFIA EMCLKIIALD PYHYFRHGWN IFDSIVALVS
660 670 680 690 700
LADVLFHKLS KNLSFLASLR VLRVFKLAKS WPTLNTLIKI IGHSVGALGN
710 720 730 740 750
LTVVLTIVVF IFSVVGMRLF GAKFNKTCST SPESLRRWHM GDFYHSFLVV
760 770 780 790 800
FRILCGEWIE NMWECMQEME GSPLCVIVFV LIMVVGKLVV LNLFIALLLN
810 820 830 840 850
SFSNEEKDGN PEGETRKTKV QLALDRFSRA FYFMARALQN FCCKRCRRQN
860 870 880 890 900
SPKPNEATES FAGESRDTAT LDTRSWKEYD SEMTLYTGQA GAPLAPLAKE
910 920 930 940 950
EDDMECCGEC DASPTSQPSE EAQACDLPLK TKRLPSPDDH GVEMEVFSEE
960 970 980 990 1000
DPNLTIQSAR KKSDAASMLS ECSTIDLNDI FRNLQKTVSP QKQPDRCFPK
1010 1020 1030 1040 1050
GLSCIFLCCK TIKKKSPWVL WWNLRKTCYQ IVKHSWFESF IIFVILLSSG
1060 1070 1080 1090 1100
ALIFEDVNLP SRPQVEKLLK CTDNIFTFIF LLEMILKWVA FGFRKYFTSA
1110 1120 1130 1140 1150
WCWLDFLIVV VSGLSLTNLP NLKSFRNLRA LRPLRALSQF EGMKVVVNAL
1160 1170 1180 1190 1200
MSAIPAILNV LLVCLIFWLI FCILGVNFFS GKFGRCINGT DINKYFNASN
1210 1220 1230 1240 1250
VPNQSQCLVS NYTWKVPNVN FDNVGNAYLA LLQVATYKGW LDIMNAAVDS
1260 1270 1280 1290 1300
RGKDEQPAFE ANLYAYLYFV VFIIFGSFFT LNLFIGVIID NFNQQQKKLG
1310 1320 1330 1340 1350
GQDIFMTEEQ KKYYNAMKKL GTKKPQKPIP RPLNKCQAFV FDLVTSQVFD
1360 1370 1380 1390 1400
VIILGLIVTN MIIMMAESEG QPNEVKKIFD ILNIVFVVIF TVECLIKVFA
1410 1420 1430 1440 1450
LRQHYFTNGW NLFDCVVVVL SIISTLVSGL ENSNVFPPTL FRIVRLARIG
1460 1470 1480 1490 1500
RILRLVRAAR GIRTLLFALM MSLPSLFNIG LLLFLVMFIY AIFGMNWFSK
1510 1520 1530 1540 1550
VKRGSGIDDI FNFDTFSGSM LCLFQITTSA GWDALLNPML ESKASCNSSS
1560 1570 1580 1590 1600
QESCQQPQIA IVYFVSYIII SFLIVVNMYI AVILENFNTA TEESEDPLGE
1610 1620 1630 1640 1650
DDFEIFYEIW EKFDPEATQF IQYSSLSDFA DALPEPLRVA KPNRFQFLMM
1660 1670 1680 1690 1700
DLPMVMGDRL HCMDVLFAFT TRVLGNSSGL DTMKAMMEEK FMEANPFKKL
1710 1720 1730 1740 1750
YEPIVTTTKR KEEEECAAVI QRAYRRHMEK MIKLKLKGRS SSSLQVFCNG
1760
DLSSLDVPKI KVHCD
Length:1,765
Mass (Da):201,385
Last modified:July 27, 2011 - v2
Checksum:i0A17EA3B9D86FB9C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti400A → G in BAA92154 (PubMed:10623609).Curated1
Sequence conflicti427R → K in BAA92154 (PubMed:10623609).Curated1
Sequence conflicti489N → K in BAA92154 (PubMed:10623609).Curated1
Sequence conflicti738W → R in BAA92154 (PubMed:10623609).Curated1
Sequence conflicti761N → T in BAA92154 (PubMed:10623609).Curated1
Sequence conflicti764E → D in BAA92154 (PubMed:10623609).Curated1
Sequence conflicti843C → R in BAA92154 (PubMed:10623609).Curated1
Sequence conflicti1023 – 1024NL → IF in BAA92154 (PubMed:10623609).Curated2
Sequence conflicti1054F → L in BAA92154 (PubMed:10623609).Curated1
Sequence conflicti1113G → V in AAD53403 (PubMed:10444332).Curated1
Sequence conflicti1113G → V in BAA92154 (PubMed:10623609).Curated1
Sequence conflicti1212Y → H in BAA92154 (PubMed:10623609).Curated1
Sequence conflicti1376K → Q in BAA92154 (PubMed:10623609).Curated1
Sequence conflicti1496N → S in BAA92154 (PubMed:10623609).Curated1
Sequence conflicti1572F → L in BAA92154 (PubMed:10623609).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF118044 mRNA. Translation: AAD53403.1.
AB031389 mRNA. Translation: BAA92154.1.
AC124662 Genomic DNA. No translation available.
AC162937 Genomic DNA. No translation available.
CCDSiCCDS40804.1.
RefSeqiNP_036017.3. NM_011887.3.
UniGeneiMm.469833.
Mm.89981.

Genome annotation databases

EnsembliENSMUST00000070617; ENSMUSP00000065466; ENSMUSG00000034115.
GeneIDi24046.
KEGGimmu:24046.
UCSCiuc009sbk.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF118044 mRNA. Translation: AAD53403.1.
AB031389 mRNA. Translation: BAA92154.1.
AC124662 Genomic DNA. No translation available.
AC162937 Genomic DNA. No translation available.
CCDSiCCDS40804.1.
RefSeqiNP_036017.3. NM_011887.3.
UniGeneiMm.469833.
Mm.89981.

3D structure databases

ProteinModelPortaliQ9R053.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi204861. 1 interactor.
STRINGi10090.ENSMUSP00000065466.

PTM databases

iPTMnetiQ9R053.
PhosphoSitePlusiQ9R053.

Proteomic databases

PaxDbiQ9R053.
PRIDEiQ9R053.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000070617; ENSMUSP00000065466; ENSMUSG00000034115.
GeneIDi24046.
KEGGimmu:24046.
UCSCiuc009sbk.1. mouse.

Organism-specific databases

CTDi11280.
MGIiMGI:1345149. Scn11a.

Phylogenomic databases

eggNOGiKOG2301. Eukaryota.
ENOG410XNP6. LUCA.
GeneTreeiENSGT00830000128242.
HOGENOMiHOG000231755.
HOVERGENiHBG053100.
InParanoidiQ9R053.
KOiK04843.
OMAiLENFNTA.
OrthoDBiEOG091G00FK.
TreeFamiTF323985.

Miscellaneous databases

ChiTaRSiScn11a. mouse.
PROiQ9R053.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000034115.
CleanExiMM_SCN11A.
GenevisibleiQ9R053. MM.

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_MOUSE
AccessioniPrimary (citable) accession number: Q9R053
Secondary accession number(s): E9QM88, Q9JMD4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 21, 2004
Last sequence update: July 27, 2011
Last modified: November 2, 2016
This is version 118 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.