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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)DescriptionActionsGraphical viewLength
Topological domaini31 – 382ExtracellularCuratedAdd BLAST352
Transmembranei383 – 403HelicalSequence analysisAdd BLAST21
Topological domaini404 – 956CytoplasmicCuratedAdd BLAST553

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi89W → N: Abolishes interaction with FLRT2; when associated with T-91. 1 Publication1
Mutagenesisi91H → T: Abolishes interaction with FLRT2; when associated with N-89. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 30Sequence analysisAdd BLAST30
ChainiPRO_000043458031 – 956Netrin receptor UNC5DAdd BLAST926

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi73 ↔ 134Combined sources
Disulfide bondi85 ↔ 132Combined sources
Glycosylationi115N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi178 ↔ 229PROSITE-ProRule annotationBy similarity
Glycosylationi226N-linked (GlcNAc...)Sequence analysis1
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)DescriptionActionsGraphical viewLength
Sitei419 – 420Cleavage; by caspase-3Curated2

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiF1LW30.

Expressioni

Gene expression databases

BgeeiENSRNOG00000011858.

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

1956
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi53 – 56Combined sources4
Beta strandi61 – 66Combined sources6
Beta strandi69 – 77Combined sources9
Beta strandi79 – 85Combined sources7
Helixi92 – 94Combined sources3
Beta strandi95 – 101Combined sources7
Beta strandi103 – 106Combined sources4
Beta strandi108 – 116Combined sources9
Helixi118 – 123Combined sources6
Beta strandi131 – 137Combined sources7
Beta strandi139 – 152Combined sources14
Beta strandi174 – 177Combined sources4
Beta strandi183 – 185Combined sources3
Beta strandi188 – 197Combined sources10
Turni200 – 202Combined sources3
Beta strandi206 – 208Combined sources3
Beta strandi212 – 222Combined sources11
Beta strandi225 – 232Combined sources8
Beta strandi237 – 239Combined sources3
Beta strandi243 – 247Combined sources5
Beta strandi263 – 274Combined sources12
Beta strandi283 – 285Combined sources3
Beta strandi293 – 301Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4V2BX-ray2.00A/B1-161[»]
4V2CX-ray4.00B/D1-161[»]
5FTTX-ray3.40A/E32-307[»]
5FTUX-ray6.01A/E/I32-161[»]
SMRiF1LW30.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini52 – 149Ig-likePROSITE-ProRule annotationAdd BLAST98
Domaini164 – 242Ig-like C2-typePROSITE-ProRule annotationAdd BLAST79
Domaini250 – 304TSP type-1 1PROSITE-ProRule annotationAdd BLAST55
Domaini306 – 358TSP type-1 2PROSITE-ProRule annotationAdd BLAST53
Domaini543 – 648ZU5PROSITE-ProRule annotationAdd BLAST106
Domaini862 – 939DeathCuratedAdd BLAST78

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni89 – 91Important for interaction with FLRT21 Publication3

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.
OrthoDBiEOG091G040Q.
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.
IPR033772. UPA.
IPR000906. ZU5_dom.
[Graphical view]
PfamiPF00531. Death. 1 hit.
PF07679. I-set. 1 hit.
PF00090. TSP_1. 2 hits.
PF17217. UPA. 1 hit.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4V2BX-ray2.00A/B1-161[»]
4V2CX-ray4.00B/D1-161[»]
5FTTX-ray3.40A/E32-307[»]
5FTUX-ray6.01A/E/I32-161[»]
SMRiF1LW30.
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.
OrthoDBiEOG091G040Q.
TreeFamiTF316767.

Miscellaneous databases

PROiF1LW30.

Gene expression databases

BgeeiENSRNOG00000011858.

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.
IPR033772. UPA.
IPR000906. ZU5_dom.
[Graphical view]
PfamiPF00531. Death. 1 hit.
PF07679. I-set. 1 hit.
PF00090. TSP_1. 2 hits.
PF17217. UPA. 1 hit.
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...

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: November 30, 2016
This is version 44 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.