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Nephrin (Renal glomerulus-specific cell adhesion receptor)

 NPHN_RAT                Reviewed;        1252 AA.
Q9R044; Q9JIX2; Q9QXX7;
16-APR-2002, integrated into UniProtKB/Swiss-Prot.
08-MAR-2011, sequence version 2.
20-JUN-2018, entry version 150.
RecName: Full=Nephrin;
AltName: Full=Renal glomerulus-specific cell adhesion receptor;
Flags: Precursor;
Name=Nphs1; Synonyms=Nphn;
Rattus norvegicus (Rat).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Rattus.
NCBI_TaxID=10116;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
TISSUE=Kidney;
PubMed=10820162;
Putaala H., Sainio K., Sariola H., Tryggvason K.;
"Primary structure of mouse and rat nephrin cDNA and structure and
expression of the mouse gene.";
J. Am. Soc. Nephrol. 11:991-1001(2000).
[2]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), AND SUBCELLULAR LOCATION.
STRAIN=Wistar; TISSUE=Renal glomerulus;
PubMed=10792613; DOI=10.1046/j.1523-1755.2000.00044.x;
Kawachi H., Koike H., Kurihara H., Yaoita E., Orikasa M., Shia M.A.,
Sakai T., Yamamoto T., Salant D.J., Shimizu F.;
"Cloning of rat nephrin: expression in developing glomeruli and in
proteinuric states.";
Kidney Int. 57:1949-1961(2000).
[3]
NUCLEOTIDE SEQUENCE [MRNA] OF 19-1252 (ISOFORMS 1; 2 AND 3), FUNCTION,
AND TISSUE SPECIFICITY.
STRAIN=Sprague-Dawley; TISSUE=Renal glomerulus;
PubMed=10487848; DOI=10.1016/S0002-9440(10)65190-5;
Ahola H., Wang S.-X., Luimula P., Solin M.-L., Holzman L.B.,
Holthoefer H.;
"Cloning and expression of the rat nephrin homolog.";
Am. J. Pathol. 155:907-913(1999).
[4]
INDUCTION, AND TISSUE SPECIFICITY.
STRAIN=Sprague-Dawley; TISSUE=Kidney;
PubMed=11012881; DOI=10.1046/j.1523-1755.2000.00308.x;
Luimula P., Ahola H., Wang S.X., Solin M.L., Aaltonen P., Tikkanen I.,
Kerjaschki D., Holthofer H.;
"Nephrin in experimental glomerular disease.";
Kidney Int. 58:1461-1468(2000).
[5]
FUNCTION.
PubMed=11880318; DOI=10.1152/ajprenal.00290.2001;
Yuan H., Takeuchi E., Salant D.J.;
"Podocyte slit-diaphragm protein nephrin is linked to the actin
cytoskeleton.";
Am. J. Physiol. 282:F585-F591(2002).
[6]
INTERACTION WITH MAGI1.
PubMed=16155592; DOI=10.1038/labinvest.3700347;
Hirabayashi S., Mori H., Kansaku A., Kurihara H., Sakai T.,
Shimizu F., Kawachi H., Hata Y.;
"MAGI-1 is a component of the glomerular slit diaphragm that is
tightly associated with nephrin.";
Lab. Invest. 85:1528-1543(2005).
[7]
INTERACTION WITH ACTN4; CASK; IQGAP1; MAGI2; SPTAN1 AND SPTBN1.
STRAIN=Sprague-Dawley; TISSUE=Renal glomerulus;
PubMed=15994232; DOI=10.1073/pnas.0504166102;
Lehtonen S., Ryan J.J., Kudlicka K., Iino N., Zhou H., Farquhar M.G.;
"Cell junction-associated proteins IQGAP1, MAGI-2, CASK, spectrins,
and alpha-actinin are components of the nephrin multiprotein
complex.";
Proc. Natl. Acad. Sci. U.S.A. 102:9814-9819(2005).
[8]
INTERACTION WITH DDN.
PubMed=17537921; DOI=10.1073/pnas.0700917104;
Asanuma K., Campbell K.N., Kim K., Faul C., Mundel P.;
"Nuclear relocation of the nephrin and CD2AP-binding protein dendrin
promotes apoptosis of podocytes.";
Proc. Natl. Acad. Sci. U.S.A. 104:10134-10139(2007).
[9]
PHOSPHORYLATION AT TYR-1204 BY FYN.
PubMed=19179337; DOI=10.1074/jbc.M806851200;
Harita Y., Kurihara H., Kosako H., Tezuka T., Sekine T., Igarashi T.,
Ohsawa I., Ohta S., Hattori S.;
"Phosphorylation of nephrin triggers Ca2+ signaling by recruitment and
activation of phospholipase C-{gamma}1.";
J. Biol. Chem. 284:8951-8962(2009).
[10]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1112; THR-1115 AND
SER-1119, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
PubMed=22673903; DOI=10.1038/ncomms1871;
Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A.,
Lundby C., Olsen J.V.;
"Quantitative maps of protein phosphorylation sites across 14
different rat organs and tissues.";
Nat. Commun. 3:876-876(2012).
-!- FUNCTION: Seems to play a role in the development or function of
the kidney glomerular filtration barrier. Regulates glomerular
vascular permeability. May anchor the podocyte slit diaphragm to
the actin cytoskeleton. Plays a role in skeletal muscle formation
through regulation of myoblast fusion.
{ECO:0000269|PubMed:10487848, ECO:0000269|PubMed:11880318}.
-!- SUBUNIT: Interacts with NPHS2 and with CD2AP (via C-terminal
domain). Self-associates (via the Ig-like domains). Also interacts
(via the Ig-like domains) with KIRREL1/NEPH1 and KIRREL2; the
interaction with KIRREL1 is dependent on KIRREL1 glycosylation.
Interacts with KIRREL3 (By similarity). Interacts with MAGI1 (via
PDZ 2 and 3 domains) forming a tripartite complex with IGSF5/JAM4.
Interacts with DDN; the interaction is direct. Forms a complex
with ACTN4, CASK, IQGAP1, MAGI2, SPTAN1 and SPTBN1.
{ECO:0000250|UniProtKB:Q9QZS7, ECO:0000269|PubMed:15994232,
ECO:0000269|PubMed:16155592, ECO:0000269|PubMed:17537921}.
-!- INTERACTION:
P97710:Sirpa; NbExp=2; IntAct=EBI-7945021, EBI-7945080;
-!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Single-pass
type I membrane protein {ECO:0000305}. Note=Located at podocyte
slit diaphragm between podocyte foot processes.
{ECO:0000269|PubMed:10792613}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=3;
Comment=Experimental confirmation may be lacking for some
isoforms.;
Name=1;
IsoId=Q9R044-1; Sequence=Displayed;
Name=2; Synonyms=Alpha;
IsoId=Q9R044-2; Sequence=VSP_002599;
Name=3; Synonyms=Beta;
IsoId=Q9R044-3; Sequence=VSP_002600;
-!- TISSUE SPECIFICITY: Strongly expressed in the podocytes of kidney
glomeruli (at protein level) and at lower levels in the spleen.
{ECO:0000269|PubMed:10487848, ECO:0000269|PubMed:11012881}.
-!- INDUCTION: Following injection with puromycin which induces
nephrosis, down-regulated by 40% 3 days post-injection and by 80%
at day 10. Also down-regulated by HgCl2 with rapid decrease at day
3. {ECO:0000269|PubMed:11012881}.
-!- PTM: Phosphorylated at Tyr-1204 by FYN, leading to the recruitment
and activation of phospholipase C-gamma-1/PLCG1.
{ECO:0000269|PubMed:19179337}.
-!- SIMILARITY: Belongs to the immunoglobulin superfamily.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AF172255; AAF91086.1; -; mRNA.
EMBL; AF161715; AAF14884.1; -; mRNA.
EMBL; AF125521; AAF12734.1; -; mRNA.
RefSeq; NP_072150.1; NM_022628.1.
UniGene; Rn.48745; -.
ProteinModelPortal; Q9R044; -.
SMR; Q9R044; -.
BioGrid; 249144; 8.
CORUM; Q9R044; -.
IntAct; Q9R044; 1.
MINT; Q9R044; -.
STRING; 10116.ENSRNOP00000049922; -.
iPTMnet; Q9R044; -.
PhosphoSitePlus; Q9R044; -.
PaxDb; Q9R044; -.
PRIDE; Q9R044; -.
GeneID; 64563; -.
KEGG; rno:64563; -.
UCSC; RGD:620460; rat. [Q9R044-1]
CTD; 4868; -.
RGD; 620460; Nphs1.
eggNOG; KOG3515; Eukaryota.
eggNOG; ENOG410XRJN; LUCA.
HOGENOM; HOG000113844; -.
HOVERGEN; HBG031752; -.
InParanoid; Q9R044; -.
PhylomeDB; Q9R044; -.
PRO; PR:Q9R044; -.
Proteomes; UP000002494; Unplaced.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
GO; GO:0016020; C:membrane; IDA:RGD.
GO; GO:0045121; C:membrane raft; IDA:RGD.
GO; GO:0005886; C:plasma membrane; IDA:UniProtKB.
GO; GO:0032991; C:protein-containing complex; IDA:RGD.
GO; GO:0036057; C:slit diaphragm; IDA:UniProtKB.
GO; GO:0051393; F:alpha-actinin binding; IPI:RGD.
GO; GO:0019904; F:protein domain specific binding; IPI:RGD.
GO; GO:0030507; F:spectrin binding; IPI:RGD.
GO; GO:0007155; P:cell adhesion; IEA:UniProtKB-KW.
GO; GO:0003094; P:glomerular filtration; IC:UniProtKB.
GO; GO:0007517; P:muscle organ development; IEA:UniProtKB-KW.
CDD; cd00063; FN3; 1.
Gene3D; 2.60.40.10; -; 10.
InterPro; IPR013162; CD80_C2-set.
InterPro; IPR003961; FN3_dom.
InterPro; IPR036116; FN3_sf.
InterPro; IPR007110; Ig-like_dom.
InterPro; IPR036179; Ig-like_dom_sf.
InterPro; IPR013783; Ig-like_fold.
InterPro; IPR003599; Ig_sub.
InterPro; IPR003598; Ig_sub2.
Pfam; PF08205; C2-set_2; 4.
Pfam; PF00041; fn3; 1.
SMART; SM00060; FN3; 1.
SMART; SM00409; IG; 8.
SMART; SM00408; IGc2; 7.
SUPFAM; SSF48726; SSF48726; 9.
SUPFAM; SSF49265; SSF49265; 1.
PROSITE; PS50853; FN3; 1.
PROSITE; PS50835; IG_LIKE; 7.
1: Evidence at protein level;
Alternative splicing; Cell adhesion; Cell membrane; Complete proteome;
Developmental protein; Disulfide bond; Glycoprotein;
Immunoglobulin domain; Membrane; Myogenesis; Phosphoprotein;
Reference proteome; Repeat; Signal; Transmembrane;
Transmembrane helix.
SIGNAL 1 35 {ECO:0000255}.
CHAIN 36 1252 Nephrin.
/FTId=PRO_0000015054.
TOPO_DOM 36 1078 Extracellular. {ECO:0000255}.
TRANSMEM 1079 1099 Helical. {ECO:0000255}.
TOPO_DOM 1100 1252 Cytoplasmic. {ECO:0000255}.
DOMAIN 39 144 Ig-like C2-type 1.
DOMAIN 149 247 Ig-like C2-type 2.
DOMAIN 256 347 Ig-like C2-type 3.
DOMAIN 354 448 Ig-like C2-type 4.
DOMAIN 454 554 Ig-like C2-type 5.
DOMAIN 558 649 Ig-like C2-type 6.
DOMAIN 754 846 Ig-like C2-type 7.
DOMAIN 852 953 Ig-like C2-type 8.
DOMAIN 957 1052 Fibronectin type-III.
{ECO:0000255|PROSITE-ProRule:PRU00316}.
MOD_RES 446 446 Phosphoserine.
{ECO:0000250|UniProtKB:O60500}.
MOD_RES 1112 1112 Phosphoserine.
{ECO:0000244|PubMed:22673903}.
MOD_RES 1115 1115 Phosphothreonine.
{ECO:0000244|PubMed:22673903}.
MOD_RES 1119 1119 Phosphoserine.
{ECO:0000244|PubMed:22673903}.
MOD_RES 1204 1204 Phosphotyrosine; by FYN.
{ECO:0000269|PubMed:19179337}.
CARBOHYD 54 54 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 370 370 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 561 561 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 578 578 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 591 591 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 722 722 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
DISULFID 67 125 {ECO:0000255|PROSITE-ProRule:PRU00114}.
DISULFID 174 231 {ECO:0000255|PROSITE-ProRule:PRU00114}.
DISULFID 279 331 {ECO:0000255|PROSITE-ProRule:PRU00114}.
DISULFID 375 431 {ECO:0000255|PROSITE-ProRule:PRU00114}.
DISULFID 479 542 {ECO:0000255|PROSITE-ProRule:PRU00114}.
DISULFID 581 637 {ECO:0000255|PROSITE-ProRule:PRU00114}.
DISULFID 775 830 {ECO:0000255|PROSITE-ProRule:PRU00114}.
DISULFID 877 934 {ECO:0000255|PROSITE-ProRule:PRU00114}.
VAR_SEQ 1070 1155 Missing (in isoform 3).
{ECO:0000303|PubMed:10487848}.
/FTId=VSP_002600.
VAR_SEQ 1070 1082 Missing (in isoform 2).
{ECO:0000303|PubMed:10487848}.
/FTId=VSP_002599.
CONFLICT 19 19 M -> T (in Ref. 2; AAF14884).
{ECO:0000305}.
CONFLICT 46 46 R -> Q (in Ref. 2; AAF14884).
{ECO:0000305}.
CONFLICT 1229 1229 D -> N (in Ref. 3; AAF12734).
{ECO:0000305}.
SEQUENCE 1252 AA; 136281 MW; 6A3550AB907883EC CRC64;
MGAKRVTVRG ARTSPIHRMS SLTPLLLMGM LTSGLAESPV PTSAPRGFWA LSENLTAVEG
TTVKLWCGVR APGSVVQWAK DGLLLGPNPK MPGFPRYSLE GDRAKGEFHL LIEACDLSDD
AEYECQVGRS ELGPELVSPK VILSILVSPK VLLLTPEAGS TVTWVAGQEY VVTCVSGDAK
PAPDITFIQS GRTILDVSSN VNEGSEEKLC ITEAEARVIP QSSDNGQLLV CEGSNPALDT
PIKASFTMNI LFPPGPPVID WPGLNEGHVR AGENLELPCT ARGGNPPATL QWLKNGKPVS
TAWGTEHAQA VAHSVLVMTV RPEDHGARLS CQSYNSVSAG TQERSITLQV TFPPSAITIL
GSVSQSENKN VTLCCLTKSS RPRVLLRWWL GGRQLLPTDE TVMDGLHGGH ISMSNLTFLV
RREDNGLPLT CEAFSDAFSK ETFKKSLTLN VKYPAQKLWI EGPPEGQYIR TGTRVRLVCL
AIGGNPDPSL IWFKDSRPVS EPRQPQEPRR VQLGSVEKSG STFSRELVLI IGPPDNRAKF
SCKAGQLSAS TQLVVQFPPT NLTILANSSA LRPGDALNLT CVSISSNPPV NLSWDKEGER
LEDVAAKPQS APFKGSAASR SVFLRVSSRD HGQRVTCRAH SEALRETVSS FYRFNVLYPP
EFLGEQVRAV TVVEQGQVLL PVSVSANPAP EAFNWTFRGY RLSPAGGPRH RILSGGALQL
WNVTRADDGF YQLHCQNSEG TAEALLKLDV HYAPTIRALR DPTEVNVGGS VDIVCTVDAN
PILPEMFSWE RLGEEEEDLN LDDMEKVSKG STGRLRIRQA KLSQAGAYQC IVDNGVAPAA
RGLVRLVVRF APQVDQPTPL TKVAAAGDST SSATLHCRAR GVPNIDFTWT KNGVPLDLQD
PRYTEHRYHQ GVVHSSLLTI ANVSAAQDYA LFKCTATNAL GSDHTNIQLV SISRPDPPLG
LKVVSISPHS VGLEWKPGFD GGLPQRFQIR YEALETPGFL HVDVLPTQAT TFTLTGLKPS
TRYRIWLLAS NALGDSGLTD KGIQVSVTTP GPDQAPEDTD HQLPTELPPG PPRLPLLPVL
FAVGGLLLLS NASCVGGLLW RRRLRRLAEE ISEKTEAGSE DRIRNEYEES QWTGDRDTRS
STVSTAEVDP NYYSMRDFSP QLPPTLEEVL YHQGAEGEDM AFPGHLHDEV ERAYGPPGAW
GPLYDEVRMD PYDLRWPEVQ CEDPRGIYDQ VAADMDAVEA SSLPFELRGH LV


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