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Protein

Sodium channel protein type 2 subunit alpha

Gene

Scn2a

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.2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei1489Important for channel closure1

GO - Molecular functioni

  • leucine zipper domain binding Source: RGD
  • sodium ion binding Source: RGD
  • voltage-gated sodium channel activity Source: UniProtKB

GO - Biological processi

  • membrane depolarization during action potential Source: GO_Central
  • myelination Source: BHF-UCL
  • neuronal action potential Source: RGD
  • sodium ion transmembrane transport Source: UniProtKB
  • sodium ion transport Source: RGD
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 2 subunit alpha
Alternative name(s):
Sodium channel protein brain II subunit alpha
Sodium channel protein type II subunit alpha
Voltage-gated sodium channel subunit alpha Nav1.2
Gene namesi
Name:Scn2a
Synonyms:Scn2a1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi3632. Scn2a.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 124CytoplasmicSequence analysisAdd BLAST124
Transmembranei125 – 148Helical; Name=S1 of repeat ISequence analysisAdd BLAST24
Topological domaini149 – 156ExtracellularSequence analysis8
Transmembranei157 – 176Helical; Name=S2 of repeat ISequence analysisAdd BLAST20
Topological domaini177 – 189CytoplasmicSequence analysisAdd BLAST13
Transmembranei190 – 208Helical; Name=S3 of repeat ISequence analysisAdd BLAST19
Topological domaini209 – 214ExtracellularSequence analysis6
Transmembranei215 – 234Helical; Voltage-sensor; Name=S4 of repeat ISequence analysisAdd BLAST20
Topological domaini235 – 250CytoplasmicSequence analysisAdd BLAST16
Transmembranei251 – 274Helical; Name=S5 of repeat ISequence analysisAdd BLAST24
Topological domaini275 – 401ExtracellularSequence analysisAdd BLAST127
Transmembranei402 – 427Helical; Name=S6 of repeat ISequence analysisAdd BLAST26
Topological domaini428 – 753CytoplasmicSequence analysisAdd BLAST326
Transmembranei754 – 778Helical; Name=S1 of repeat IISequence analysisAdd BLAST25
Topological domaini779 – 789ExtracellularSequence analysisAdd BLAST11
Transmembranei790 – 813Helical; Name=S2 of repeat IISequence analysisAdd BLAST24
Topological domaini814 – 821CytoplasmicSequence analysis8
Transmembranei822 – 841Helical; Name=S3 of repeat IISequence analysisAdd BLAST20
Topological domaini842 – 847ExtracellularSequence analysis6
Transmembranei848 – 867Helical; Voltage-sensor; Name=S4 of repeat IISequence analysisAdd BLAST20
Topological domaini868 – 883CytoplasmicSequence analysisAdd BLAST16
Transmembranei884 – 904Helical; Name=S5 of repeat IISequence analysisAdd BLAST21
Topological domaini905 – 957ExtracellularSequence analysisAdd BLAST53
Transmembranei958 – 983Helical; Name=S6 of repeat IISequence analysisAdd BLAST26
Topological domaini984 – 1203CytoplasmicSequence analysisAdd BLAST220
Transmembranei1204 – 1227Helical; Name=S1 of repeat IIISequence analysisAdd BLAST24
Topological domaini1228 – 1240ExtracellularSequence analysisAdd BLAST13
Transmembranei1241 – 1266Helical; Name=S2 of repeat IIISequence analysisAdd BLAST26
Topological domaini1267 – 1272CytoplasmicSequence analysis6
Transmembranei1273 – 1294Helical; Name=S3 of repeat IIISequence analysisAdd BLAST22
Topological domaini1295 – 1298ExtracellularSequence analysis4
Transmembranei1299 – 1320Helical; Voltage-sensor; Name=S4 of repeat IIISequence analysisAdd BLAST22
Topological domaini1321 – 1339CytoplasmicSequence analysisAdd BLAST19
Transmembranei1340 – 1367Helical; Name=S5 of repeat IIISequence analysisAdd BLAST28
Topological domaini1368 – 1446ExtracellularSequence analysisAdd BLAST79
Transmembranei1447 – 1473Helical; Name=S6 of repeat IIISequence analysisAdd BLAST27
Topological domaini1474 – 1526CytoplasmicSequence analysisAdd BLAST53
Transmembranei1527 – 1550Helical; Name=S1 of repeat IVSequence analysisAdd BLAST24
Topological domaini1551 – 1561ExtracellularSequence analysisAdd BLAST11
Transmembranei1562 – 1585Helical; Name=S2 of repeat IVSequence analysisAdd BLAST24
Topological domaini1586 – 1591CytoplasmicSequence analysis6
Transmembranei1592 – 1615Helical; Name=S3 of repeat IVSequence analysisAdd BLAST24
Topological domaini1616 – 1625ExtracellularSequence analysis10
Transmembranei1626 – 1647Helical; Voltage-sensor; Name=S4 of repeat IVSequence analysisAdd BLAST22
Topological domaini1648 – 1662CytoplasmicSequence analysisAdd BLAST15
Transmembranei1663 – 1685Helical; Name=S5 of repeat IVSequence analysisAdd BLAST23
Topological domaini1686 – 1751ExtracellularSequence analysisAdd BLAST66
Transmembranei1752 – 1776Helical; Name=S6 of repeat IVSequence analysisAdd BLAST25
Topological domaini1777 – 2005CytoplasmicSequence analysisAdd BLAST229

GO - Cellular componenti

  • axon initial segment Source: RGD
  • intrinsic component of plasma membrane Source: UniProtKB
  • neuron projection Source: RGD
  • node of Ranvier Source: BHF-UCL
  • sodium channel complex Source: UniProtKB
  • voltage-gated sodium channel complex Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1489F → Q: Strongly impairs channel inactivation. 1 Publication1
Mutagenesisi1506S → A: Blocks the reduction of Na+ current and the slowing of inactivation caused by PKC. 1 Publication1
Mutagenesisi1975Y → A: Abolishes interaction with NEDD4L. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL3399.
GuidetoPHARMACOLOGYi579.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000484921 – 2005Sodium channel protein type 2 subunit alphaAdd BLAST2005

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei4Phosphoserine1 Publication1
Glycosylationi212N-linked (GlcNAc...)Sequence analysis1
Glycosylationi285N-linked (GlcNAc...)Sequence analysis1
Glycosylationi291N-linked (GlcNAc...)Sequence analysis1
Glycosylationi297N-linked (GlcNAc...)Sequence analysis1
Glycosylationi303N-linked (GlcNAc...)Sequence analysis1
Glycosylationi308N-linked (GlcNAc...)Sequence analysis1
Glycosylationi340N-linked (GlcNAc...)Sequence analysis1
Modified residuei468Phosphoserine1 Publication1
Modified residuei471Phosphoserine1 Publication1
Modified residuei484PhosphoserineCombined sources1 Publication1
Modified residuei526PhosphoserineCombined sources1
Modified residuei528PhosphoserineCombined sources1 Publication1
Modified residuei531PhosphoserineCombined sources1
Modified residuei553PhosphoserineCombined sources1
Modified residuei554PhosphoserineCombined sources2 Publications1
Modified residuei554Phosphoserine; by PKC; in vitro2 Publications1
Modified residuei558PhosphoserineCombined sources1
Modified residuei573Phosphoserine; by PKC; in vitro1 Publication1
Modified residuei576Phosphoserine; by PKC; in vitro1 Publication1
Modified residuei589PhosphoserineCombined sources1
Modified residuei610Phosphoserine1 Publication1
Modified residuei623Phosphoserine1 Publication1
Modified residuei687Phosphoserine1 Publication1
Modified residuei688Phosphoserine1 Publication1
Modified residuei721PhosphoserineCombined sources1 Publication1
Glycosylationi1368N-linked (GlcNAc...)Sequence analysis1
Glycosylationi1382N-linked (GlcNAc...)Sequence analysis1
Glycosylationi1393N-linked (GlcNAc...)Sequence analysis1
Modified residuei1506Phosphoserine; by PKC2 Publications1
Modified residuei1930Phosphoserine1 Publication1
Modified residuei1943PhosphothreonineCombined sources1
Modified residuei1963PhosphothreonineCombined sources1
Modified residuei1966Phosphothreonine1 Publication1
Modified residuei1971Phosphoserine1 Publication1

Post-translational modificationi

May be ubiquitinated by NEDD4L; which would promote its endocytosis.
Phosphorylation at Ser-1506 by PKC in a highly conserved cytoplasmic loop slows inactivation of the sodium channel and reduces peak sodium currents.3 Publications

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiP04775.
PRIDEiP04775.

PTM databases

iPTMnetiP04775.
PhosphoSitePlusiP04775.
SwissPalmiP04775.

Interactioni

Subunit structurei

Heterooligomer of a large alpha subunit and a smaller beta subunit. Heterooligomer with SCN4B; disulfide-linked. Interacts with NEDD4L. Interacts with CALM.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Syt1P217072EBI-2619448,EBI-458098

GO - Molecular functioni

  • leucine zipper domain binding Source: RGD

Protein-protein interaction databases

BioGridi246890. 4 interactors.
DIPiDIP-57088N.
IntActiP04775. 1 interactor.
STRINGi10116.ENSRNOP00000007069.

Chemistry databases

BindingDBiP04775.

Structurei

Secondary structure

12005
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi1492 – 1502Combined sources11
Helixi1904 – 1922Combined sources19

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BYYNMR-A1474-1526[»]
2KXWNMR-B1901-1927[»]
2M5ENMR-B1901-1927[»]
ProteinModelPortaliP04775.
SMRiP04775.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04775.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati111 – 456ICuratedAdd BLAST346
Repeati741 – 1013IICuratedAdd BLAST273
Repeati1190 – 1504IIICuratedAdd BLAST315
Repeati1513 – 1811IVCuratedAdd BLAST299
Domaini1905 – 1934IQPROSITE-ProRule annotationAdd BLAST30

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.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG2301. Eukaryota.
ENOG410XNP6. LUCA.
HOGENOMiHOG000231755.
HOVERGENiHBG053100.
InParanoidiP04775.
KOiK04834.
PhylomeDBiP04775.

Family and domain databases

Gene3Di1.20.120.350. 4 hits.
InterProiIPR027359. Channel_four-helix_dom.
IPR005821. Ion_trans_dom.
IPR000048. IQ_motif_EF-hand-BS.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
IPR024583. Na_trans_cytopl.
[Graphical view]
PfamiPF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
PF11933. Na_trans_cytopl. 1 hit.
[Graphical view]
PRINTSiPR00170. NACHANNEL.
SMARTiSM00015. IQ. 1 hit.
[Graphical view]
PROSITEiPS50096. IQ. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P04775-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARSVLVPPG PDSFRFFTRE SLAAIEQRIA EEKAKRPKQE RKDEDDENGP
60 70 80 90 100
KPNSDLEAGK SLPFIYGDIP PEMVSEPLED LDPYYINKKT FIVLNKGKAI
110 120 130 140 150
SRFSATSALY ILTPFNPIRK LAIKILVHSL FNVLIMCTIL TNCVFMTMSN
160 170 180 190 200
PPDWTKNVEY TFTGIYTFES LIKILARGFC LEDFTFLRNP WNWLDFTVIT
210 220 230 240 250
FAYVTEFVNL GNVSALRTFR VLRALKTISV IPGLKTIVGA LIQSVKKLSD
260 270 280 290 300
VMILTVFCLS VFALIGLQLF MGNLRNKCLQ WPPDNSTFEI NITSFFNNSL
310 320 330 340 350
DWNGTAFNRT VNMFNWDEYI EDKSHFYFLE GQNDALLCGN SSDAGQCPEG
360 370 380 390 400
YICVKAGRNP NYGYTSFDTF SWAFLSLFRL MTQDFWENLY QLTLRAAGKT
410 420 430 440 450
YMIFFVLVIF LGSFYLINLI LAVVAMAYEE QNQATLEEAE QKEAEFQQML
460 470 480 490 500
EQLKKQQEEA QAAAAAASAE SRDFSGAGGI GVFSESSSVA SKLSSKSEKE
510 520 530 540 550
LKNRRKKKKQ KEQAGEEEKE DAVRKSASED SIRKKGFQFS LEGSRLTYEK
560 570 580 590 600
RFSSPHQSLL SIRGSLFSPR RNSRASLFNF KGRVKDIGSE NDFADDEHST
610 620 630 640 650
FEDNDSRRDS LFVPHRHGER RPSNVSQASR ASRGIPTLPM NGKMHSAVDC
660 670 680 690 700
NGVVSLVGGP SALTSPVGQL LPEGTTTETE IRKRRSSSYH VSMDLLEDPS
710 720 730 740 750
RQRAMSMASI LTNTMEELEE SRQKCPPCWY KFANMCLIWD CCKPWLKVKH
760 770 780 790 800
VVNLVVMDPF VDLAITICIV LNTLFMAMEH YPMTEQFSSV LSVGNLVFTG
810 820 830 840 850
IFTAEMFLKI IAMDPYYYFQ EGWNIFDGFI VSLSLMELGL ANVEGLSVLR
860 870 880 890 900
SFRLLRVFKL AKSWPTLNML IKIIGNSVGA LGNLTLVLAI IVFIFAVVGM
910 920 930 940 950
QLFGKSYKEC VCKISNDCEL PRWHMHHFFH SFLIVFRVLC GEWIETMWDC
960 970 980 990 1000
MEVAGQTMCL TVFMMVMVIG NLVVLNLFLA LLLSSFSSDN LAATDDDNEM
1010 1020 1030 1040 1050
NNLQIAVGRM QKGIDFVKRK IREFIQKAFV RKQKALDEIK PLEDLNNKKD
1060 1070 1080 1090 1100
SCISNHTTIE IGKDLNYLKD GNGTTSGIGS SVEKYVVDES DYMSFINNPS
1110 1120 1130 1140 1150
LTVTVPIALG ESDFENLNTE EFSSESDMEE SKEKLNATSS SEGSTVDIGA
1160 1170 1180 1190 1200
PAEGEQPEAE PEESLEPEAC FTEDCVRKFK CCQISIEEGK GKLWWNLRKT
1210 1220 1230 1240 1250
CYKIVEHNWF ETFIVFMILL SSGALAFEDI YIEQRKTIKT MLEYADKVFT
1260 1270 1280 1290 1300
YIFILEMLLK WVAYGFQMYF TNAWCWLDFL IVDVSLVSLT ANALGYSELG
1310 1320 1330 1340 1350
AIKSLRTLRA LRPLRALSRF EGMRVVVNAL LGAIPSIMNV LLVCLIFWLI
1360 1370 1380 1390 1400
FSIMGVNLFA GKFYHCINYT TGEMFDVSVV NNYSECQALI ESNQTARWKN
1410 1420 1430 1440 1450
VKVNFDNVGL GYLSLLQVAT FKGWMDIMYA AVDSRNVELQ PKYEDNLYMY
1460 1470 1480 1490 1500
LYFVIFIIFG SFFTLNLFIG VIIDNFNQQK KKFGGQDIFM TEEQKKYYNA
1510 1520 1530 1540 1550
MKKLGSKKPQ KPIPRPANKF QGMVFDFVTK QVFDISIMIL ICLNMVTMMV
1560 1570 1580 1590 1600
ETDDQSQEMT NILYWINLVF IVLFTGECVL KLISLRHYYF TIGWNIFDFV
1610 1620 1630 1640 1650
VVILSIVGMF LAELIEKYFV SPTLFRVIRL ARIGRILRLI KGAKGIRTLL
1660 1670 1680 1690 1700
FALMMSLPAL FNIGLLLFLV MFIYAIFGMS NFAYVKREVG IDDMFNFETF
1710 1720 1730 1740 1750
GNSMICLFQI TTSAGWDGLL APILNSGPPD CDPEKDHPGS SVKGDCGNPS
1760 1770 1780 1790 1800
VGIFFFVSYI IISFLVVVNM YIAVILENFS VATEESAEPL SEDDFEMFYE
1810 1820 1830 1840 1850
VWEKFDPDAT QFIEFCKLSD FAAALDPPLL IAKPNKVQLI AMDLPMVSGD
1860 1870 1880 1890 1900
RIHCLDILFA FTKRVLGESG EMDALRIQME ERFMASNPSK VSYEPITTTL
1910 1920 1930 1940 1950
KRKQEEVSAI VIQRAYRRYL LKQKVKKVSS IYKKDKGKED EGTPIKEDII
1960 1970 1980 1990 2000
TDKLNENSTP EKTDVTPSTT SPPSYDSVTK PEKEKFEKDK SEKEDKGKDI

RESKK
Length:2,005
Mass (Da):227,874
Last modified:August 13, 1987 - v1
Checksum:i861BE583D79F8324
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03639 mRNA. Translation: CAA27287.1.
RefSeqiNP_036779.1. NM_012647.1.
UniGeneiRn.89192.

Genome annotation databases

GeneIDi24766.
KEGGirno:24766.
UCSCiRGD:3632. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03639 mRNA. Translation: CAA27287.1.
RefSeqiNP_036779.1. NM_012647.1.
UniGeneiRn.89192.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BYYNMR-A1474-1526[»]
2KXWNMR-B1901-1927[»]
2M5ENMR-B1901-1927[»]
ProteinModelPortaliP04775.
SMRiP04775.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi246890. 4 interactors.
DIPiDIP-57088N.
IntActiP04775. 1 interactor.
STRINGi10116.ENSRNOP00000007069.

Chemistry databases

BindingDBiP04775.
ChEMBLiCHEMBL3399.
GuidetoPHARMACOLOGYi579.

PTM databases

iPTMnetiP04775.
PhosphoSitePlusiP04775.
SwissPalmiP04775.

Proteomic databases

PaxDbiP04775.
PRIDEiP04775.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi24766.
KEGGirno:24766.
UCSCiRGD:3632. rat.

Organism-specific databases

CTDi6326.
RGDi3632. Scn2a.

Phylogenomic databases

eggNOGiKOG2301. Eukaryota.
ENOG410XNP6. LUCA.
HOGENOMiHOG000231755.
HOVERGENiHBG053100.
InParanoidiP04775.
KOiK04834.
PhylomeDBiP04775.

Miscellaneous databases

EvolutionaryTraceiP04775.
PROiP04775.

Family and domain databases

Gene3Di1.20.120.350. 4 hits.
InterProiIPR027359. Channel_four-helix_dom.
IPR005821. Ion_trans_dom.
IPR000048. IQ_motif_EF-hand-BS.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
IPR024583. Na_trans_cytopl.
[Graphical view]
PfamiPF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
PF11933. Na_trans_cytopl. 1 hit.
[Graphical view]
PRINTSiPR00170. NACHANNEL.
SMARTiSM00015. IQ. 1 hit.
[Graphical view]
PROSITEiPS50096. IQ. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSCN2A_RAT
AccessioniPrimary (citable) accession number: P04775
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: November 2, 2016
This is version 146 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.