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Protein

Netrin receptor UNC5D

Gene

Unc5d

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

Functioni

Receptor for the netrin NTN4 that promotes neuronal cell survival. Plays a role in cell-cell adhesion and cell guidance. Receptor for netrin involved in cell migration. Plays a role in axon guidance by mediating axon repulsion of neuronal growth cones in the developing nervous system upon ligand binding. May play a role in apoptosis in response to DNA damage. It also acts as a dependence receptor required for apoptosis induction when not associated with netrin ligand (By similarity). Mediates cell-cell adhesion via its interaction with FLRT3 on an adjacent cell (By similarity).By similarity

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, Receptor

Keywords - Biological processi

Apoptosis

Names & Taxonomyi

Protein namesi
Recommended name:
Netrin receptor UNC5D
Alternative name(s):
Protein unc-5 homolog D
Gene namesi
Name:Unc5dImported
OrganismiRattus norvegicus (Rat)Imported
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi1309245. Unc5d.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini31 – 382352ExtracellularCuratedAdd
BLAST
Transmembranei383 – 40321HelicalSequence analysisAdd
BLAST
Topological domaini404 – 956553CytoplasmicCuratedAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi89 – 891W → N: Abolishes interaction with FLRT2; when associated with T-91. 1 Publication
Mutagenesisi91 – 911H → T: Abolishes interaction with FLRT2; when associated with N-89. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3030Sequence analysisAdd
BLAST
Chaini31 – 956926Netrin receptor UNC5DPRO_0000434580Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi73 ↔ 134Combined sources
Disulfide bondi85 ↔ 132Combined sources
Glycosylationi115 – 1151N-linked (GlcNAc...)Sequence analysis
Disulfide bondi178 ↔ 229PROSITE-ProRule annotationBy similarity
Glycosylationi226 – 2261N-linked (GlcNAc...)Sequence analysis
Disulfide bondi262 ↔ 299PROSITE-ProRule annotation
Disulfide bondi266 ↔ 303PROSITE-ProRule annotation
Disulfide bondi277 ↔ 289PROSITE-ProRule annotation
Disulfide bondi318 ↔ 352By similarity
Disulfide bondi322 ↔ 357By similarity
Disulfide bondi330 ↔ 342By similarity

Post-translational modificationi

Proteolytically cleaved by caspases during apoptosis. The cleavage does not take place when the receptor is associated with netrin ligand. Its cleavage by caspases is required to induce apoptosis (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei419 – 4202Cleavage; by caspase-3Curated

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiF1LW30.

Expressioni

Gene expression databases

ExpressionAtlasiF1LW30. baseline and differential.

Interactioni

Subunit structurei

Interacts (via extracellular domain) with FLRT2 and FLRT3 (via extracellular domain); the interaction is direct. Has higher affinity for FLRT2 (PubMed:25374360). Identified in a complex with FLRT3 and ADGRL3; does not interact with ADGRL3 by itself (By similarity).By similarity

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000015879.

Structurei

Secondary structure

1
956
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi53 – 564Combined sources
Beta strandi61 – 666Combined sources
Beta strandi69 – 779Combined sources
Beta strandi79 – 857Combined sources
Helixi92 – 943Combined sources
Beta strandi95 – 1017Combined sources
Beta strandi103 – 1064Combined sources
Beta strandi108 – 1169Combined sources
Helixi118 – 1236Combined sources
Beta strandi131 – 1377Combined sources
Beta strandi139 – 15214Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4V2BX-ray2.00A/B1-161[»]
4V2CX-ray4.00B/D1-161[»]
5FTTX-ray3.40A/E32-307[»]
5FTUX-ray6.01A/E/I32-161[»]
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini52 – 14998Ig-likePROSITE-ProRule annotationAdd
BLAST
Domaini164 – 24279Ig-like C2-typePROSITE-ProRule annotationAdd
BLAST
Domaini250 – 30455TSP type-1 1PROSITE-ProRule annotationAdd
BLAST
Domaini306 – 35853TSP type-1 2PROSITE-ProRule annotationAdd
BLAST
Domaini543 – 648106ZU5PROSITE-ProRule annotationAdd
BLAST
Domaini862 – 93978DeathCuratedAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni89 – 913Important for interaction with FLRT21 Publication

Sequence similaritiesi

Belongs to the unc-5 family.Curated
Contains 1 death domain.Curated
Contains 2 TSP type-1 domains.PROSITE-ProRule annotation
Contains 1 ZU5 domain.PROSITE-ProRule annotation

Keywords - Domaini

Immunoglobulin domain, Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG1480. Eukaryota.
ENOG410XRS6. LUCA.
InParanoidiF1LW30.
KOiK07521.
OrthoDBiEOG7BGHJX.
TreeFamiTF316767.

Family and domain databases

Gene3Di1.10.533.10. 1 hit.
2.60.40.10. 2 hits.
InterProiIPR011029. DEATH-like_dom.
IPR000488. Death_domain.
IPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR013098. Ig_I-set.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR000884. TSP1_rpt.
IPR000906. ZU5_dom.
[Graphical view]
PfamiPF00531. Death. 1 hit.
PF07679. I-set. 1 hit.
PF00090. TSP_1. 2 hits.
PF00791. ZU5. 1 hit.
[Graphical view]
SMARTiSM00005. DEATH. 1 hit.
SM00409. IG. 1 hit.
SM00408. IGc2. 1 hit.
SM00209. TSP1. 2 hits.
SM00218. ZU5. 1 hit.
[Graphical view]
SUPFAMiSSF47986. SSF47986. 1 hit.
SSF48726. SSF48726. 2 hits.
SSF82895. SSF82895. 2 hits.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS50092. TSP1. 2 hits.
PS51145. ZU5. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

F1LW30-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGTGAADRSR GARWWLPWLG LCFWAAGAEA ARGADSGEVL PDSIPSAPGT
60 70 80 90 100
LPHFIEEPED AYIIKSNPIA LRCKARPAMQ IFFKCNGEWV HQNEHVSEES
110 120 130 140 150
LDESSGLKVR EVFINVTRQQ VEDFHGPEDY WCQCVAWSHL GTSKSRKASV
160 170 180 190 200
RIAYLRKNFE QDPQGREVPI EGMIVLHCRP PEGVPAAEVE WLKNEEPIDS
210 220 230 240 250
EQDENIDTRA DHNLIIRQAR LSDSGNYTCM AANIVAKRRS LSATVVVYVN
260 270 280 290 300
GGWSSWTEWS ACNVRCGRGW QKRSRTCTNP APLNGGAFCE GMSVQKITCT
310 320 330 340 350
ALCPVDGSWE VWSEWSVCSP ECEHLRIREC TAPPPRNGGK FCEGLSQESE
360 370 380 390 400
NCTDGLCILD KKPLHEIKPQ RWSRRGIENA SDIALYSGLG AAVVAVAVLV
410 420 430 440 450
IGVTLYRRSH SDYGVDVIDS SALTGGFQTF NFKTVRQGNS LLLNPAMHPD
460 470 480 490 500
LTVSRTYSGP ICLQDPLDKE LMTESSLFNP LSDIKVKVQS SFMVSLGVSE
510 520 530 540 550
RAEYHGKNHS GTFPHGNNRG FSTIHPRNKT PYIQNLSSLP TRTELRTTGV
560 570 580 590 600
FGHLGGRLVM PNTGVSLLIP HGAIPEENSW EIYMSINQGE PSLQSDGSEV
610 620 630 640 650
LLSPEVTCGP PDMLVTTPFA LTIPHCADVS SEHWNIHLKK RTQQGKWEEV
660 670 680 690 700
MSVEDESTSC YCLLDPFACH VLLDSFGTYA LTGEPITDCA VKQLKVAVFG
710 720 730 740 750
CMSCNSLDYN LRVYCVDNTP CAFQEVVSDE RHQGGQLLEE PKLLHFKGNT
760 770 780 790 800
FSLQISVLDI PPFLWRIKPF TACQEVPFSR VWSSNRQPLH CAFSLERYTP
810 820 830 840 850
TTTQLSCKIC IRQLKGHEQI LQVQTSILES ERETITFFAQ EDSTFPAQTG
860 870 880 890 900
PKAFKIPYSI RQRICATFDT PNAKGKDWQM LAQKNSINRN LSYFATQSSP
910 920 930 940 950
SAVILNLWEA RHQQDGDLDS LACALEEIGR THTKLSNITE PQLDDTDFNY

SRQNGL
Length:956
Mass (Da):106,520
Last modified:November 11, 2015 - v4
Checksum:iE389EEE963CEE79E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AABR06088887 Genomic DNA. No translation available.
AABR07026201 Genomic DNA. No translation available.
AABR07026202 Genomic DNA. No translation available.
AABR07026203 Genomic DNA. No translation available.
AABR07026204 Genomic DNA. No translation available.
AABR07026205 Genomic DNA. No translation available.
RefSeqiNP_001100789.2. NM_001107319.2.
UniGeneiRn.231130.

Genome annotation databases

GeneIDi306534.
KEGGirno:306534.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AABR06088887 Genomic DNA. No translation available.
AABR07026201 Genomic DNA. No translation available.
AABR07026202 Genomic DNA. No translation available.
AABR07026203 Genomic DNA. No translation available.
AABR07026204 Genomic DNA. No translation available.
AABR07026205 Genomic DNA. No translation available.
RefSeqiNP_001100789.2. NM_001107319.2.
UniGeneiRn.231130.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4V2BX-ray2.00A/B1-161[»]
4V2CX-ray4.00B/D1-161[»]
5FTTX-ray3.40A/E32-307[»]
5FTUX-ray6.01A/E/I32-161[»]
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000015879.

Proteomic databases

PaxDbiF1LW30.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi306534.
KEGGirno:306534.

Organism-specific databases

CTDi137970.
RGDi1309245. Unc5d.

Phylogenomic databases

eggNOGiKOG1480. Eukaryota.
ENOG410XRS6. LUCA.
InParanoidiF1LW30.
KOiK07521.
OrthoDBiEOG7BGHJX.
TreeFamiTF316767.

Miscellaneous databases

PROiF1LW30.

Gene expression databases

ExpressionAtlasiF1LW30. baseline and differential.

Family and domain databases

Gene3Di1.10.533.10. 1 hit.
2.60.40.10. 2 hits.
InterProiIPR011029. DEATH-like_dom.
IPR000488. Death_domain.
IPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR013098. Ig_I-set.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR000884. TSP1_rpt.
IPR000906. ZU5_dom.
[Graphical view]
PfamiPF00531. Death. 1 hit.
PF07679. I-set. 1 hit.
PF00090. TSP_1. 2 hits.
PF00791. ZU5. 1 hit.
[Graphical view]
SMARTiSM00005. DEATH. 1 hit.
SM00409. IG. 1 hit.
SM00408. IGc2. 1 hit.
SM00209. TSP1. 2 hits.
SM00218. ZU5. 1 hit.
[Graphical view]
SUPFAMiSSF47986. SSF47986. 1 hit.
SSF48726. SSF48726. 2 hits.
SSF82895. SSF82895. 2 hits.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS50092. TSP1. 2 hits.
PS51145. ZU5. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Genome sequence of the Brown Norway rat yields insights into mammalian evolution."
    Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J., Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G., Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G., Morgan M.
    , Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G., Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S., Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T., Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D., Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L., Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D., Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M., Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C., Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J., Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H., Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X., Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q., Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P., Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A., Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C., Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J., Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J., Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F., Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A., Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A., Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J., Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M., Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C., Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L., Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W., Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y., Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V., Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M., Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S., Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B., Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S., Collins F.S.
    Nature 428:493-521(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Brown Norway.
  2. "FLRT structure: balancing repulsion and cell adhesion in cortical and vascular development."
    Seiradake E., del Toro D., Nagel D., Cop F., Haertl R., Ruff T., Seyit-Bremer G., Harlos K., Border E.C., Acker-Palmer A., Jones E.Y., Klein R.
    Neuron 84:370-385(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 1-130 IN COMPLEX WITH FLRT2, INTERACTION WITH FLRT2 AND FLRT3, DISULFIDE BONDS, SUBCELLULAR LOCATION, MUTAGENESIS OF TRP-89 AND HIS-91.

Entry informationi

Entry nameiUNC5D_RAT
AccessioniPrimary (citable) accession number: F1LW30
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 11, 2015
Last sequence update: November 11, 2015
Last modified: July 6, 2016
This is version 40 of the entry and version 4 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.