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O43854

- EDIL3_HUMAN

UniProt

O43854 - EDIL3_HUMAN

Protein

EGF-like repeat and discoidin I-like domain-containing protein 3

Gene

EDIL3

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 122 (01 Oct 2014)
      Sequence version 1 (01 Jun 1998)
      Previous versions | rss
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    Functioni

    Promotes adhesion of endothelial cells through interaction with the alpha-v/beta-3 integrin receptor. Inhibits formation of vascular-like structures. May be involved in regulation of vascular morphogenesis of remodeling in embryonic development.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi119 – 1191Calcium
    Metal bindingi120 – 1201Calcium; via carbonyl oxygen
    Metal bindingi122 – 1221Calcium
    Metal bindingi136 – 1361Calcium
    Metal bindingi137 – 1371Calcium; via carbonyl oxygen

    GO - Molecular functioni

    1. calcium ion binding Source: InterPro
    2. integrin binding Source: ProtInc

    GO - Biological processi

    1. cell adhesion Source: UniProtKB-KW
    2. multicellular organismal development Source: UniProtKB-KW
    3. positive regulation of cell-substrate adhesion Source: Ensembl

    Keywords - Molecular functioni

    Developmental protein

    Keywords - Biological processi

    Cell adhesion

    Keywords - Ligandi

    Calcium, Metal-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    EGF-like repeat and discoidin I-like domain-containing protein 3
    Alternative name(s):
    Developmentally-regulated endothelial cell locus 1 protein
    Integrin-binding protein DEL1
    Gene namesi
    Name:EDIL3
    Synonyms:DEL1
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 5

    Organism-specific databases

    HGNCiHGNC:3173. EDIL3.

    Subcellular locationi

    GO - Cellular componenti

    1. extracellular vesicular exosome Source: UniProtKB

    Keywords - Cellular componenti

    Secreted

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA27613.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2323Sequence AnalysisAdd
    BLAST
    Chaini24 – 480457EGF-like repeat and discoidin I-like domain-containing protein 3PRO_0000007522Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi26 ↔ 371 Publication
    Disulfide bondi31 ↔ 481 Publication
    Disulfide bondi50 ↔ 591 Publication
    Glycosylationi73 – 731O-linked (GalNAc...)1 Publication
    Disulfide bondi78 ↔ 891 Publication
    Disulfide bondi83 ↔ 1051 Publication
    Glycosylationi88 – 881O-linked (Fuc...)1 Publication
    Disulfide bondi107 ↔ 1161 Publication
    Disulfide bondi123 ↔ 1341 Publication
    Disulfide bondi128 ↔ 1431 Publication
    Glycosylationi140 – 1401N-linked (GlcNAc...)1 Publication
    Disulfide bondi145 ↔ 1541 Publication
    Disulfide bondi158 ↔ 314By similarity
    Disulfide bondi301 ↔ 305By similarity
    Disulfide bondi319 ↔ 476By similarity

    Keywords - PTMi

    Disulfide bond, Glycoprotein

    Proteomic databases

    MaxQBiO43854.
    PaxDbiO43854.
    PRIDEiO43854.

    PTM databases

    PhosphoSiteiO43854.

    Expressioni

    Gene expression databases

    BgeeiO43854.
    CleanExiHS_EDIL3.
    GenevestigatoriO43854.

    Organism-specific databases

    HPAiHPA020415.

    Interactioni

    Protein-protein interaction databases

    BioGridi115394. 3 interactions.
    IntActiO43854. 2 interactions.
    STRINGi9606.ENSP00000296591.

    Structurei

    Secondary structure

    1
    480
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi32 – 343
    Beta strandi36 – 383
    Beta strandi47 – 493
    Turni56 – 594
    Turni66 – 705
    Beta strandi88 – 914
    Beta strandi103 – 1064
    Beta strandi111 – 1133
    Turni122 – 1254
    Beta strandi133 – 1375
    Beta strandi140 – 1445

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4D90X-ray2.60A/B24-157[»]
    ProteinModelPortaliO43854.
    SMRiO43854. Positions 26-480.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini24 – 6037EGF-like 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini74 – 11744EGF-like 2PROSITE-ProRule annotationAdd
    BLAST
    Domaini119 – 15537EGF-like 3PROSITE-ProRule annotationAdd
    BLAST
    Domaini158 – 314157F5/8 type C 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini319 – 476158F5/8 type C 2PROSITE-ProRule annotationAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi96 – 983Cell attachment site

    Domaini

    EGF2 and EGF3 form a rigid rod via an interdomain calcium ion binding site, while the long linker between EGF1 and EGF2 lends considerable flexibility to EGF1.

    Sequence similaritiesi

    Contains 3 EGF-like domains.PROSITE-ProRule annotation
    Contains 2 F5/8 type C domains.PROSITE-ProRule annotation

    Keywords - Domaini

    EGF-like domain, Repeat, Signal

    Phylogenomic databases

    eggNOGiNOG151278.
    HOGENOMiHOG000236278.
    HOVERGENiHBG002385.
    InParanoidiO43854.
    OMAiNINECEA.
    OrthoDBiEOG7ZWD1D.
    PhylomeDBiO43854.
    TreeFamiTF330156.

    Family and domain databases

    Gene3Di2.60.120.260. 2 hits.
    InterProiIPR000421. Coagulation_fac_5/8-C_type_dom.
    IPR000742. EG-like_dom.
    IPR001881. EGF-like_Ca-bd_dom.
    IPR013032. EGF-like_CS.
    IPR000152. EGF-type_Asp/Asn_hydroxyl_site.
    IPR018097. EGF_Ca-bd_CS.
    IPR008979. Galactose-bd-like.
    [Graphical view]
    PfamiPF00008. EGF. 2 hits.
    PF00754. F5_F8_type_C. 2 hits.
    [Graphical view]
    SMARTiSM00181. EGF. 2 hits.
    SM00179. EGF_CA. 1 hit.
    SM00231. FA58C. 2 hits.
    [Graphical view]
    SUPFAMiSSF49785. SSF49785. 2 hits.
    PROSITEiPS00010. ASX_HYDROXYL. 1 hit.
    PS00022. EGF_1. 2 hits.
    PS01186. EGF_2. 2 hits.
    PS50026. EGF_3. 3 hits.
    PS01187. EGF_CA. 1 hit.
    PS01285. FA58C_1. 2 hits.
    PS01286. FA58C_2. 2 hits.
    PS50022. FA58C_3. 2 hits.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

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

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: O43854-1) [UniParc]FASTAAdd to Basket

    Also known as: Long

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MKRSVAVWLL VGLSLGVPQF GKGDICDPNP CENGGICLPG LADGSFSCEC    50
    PDGFTDPNCS SVVEVASDEE EPTSAGPCTP NPCHNGGTCE ISEAYRGDTF 100
    IGYVCKCPRG FNGIHCQHNI NECEVEPCKN GGICTDLVAN YSCECPGEFM 150
    GRNCQYKCSG PLGIEGGIIS NQQITASSTH RALFGLQKWY PYYARLNKKG 200
    LINAWTAAEN DRWPWIQINL QRKMRVTGVI TQGAKRIGSP EYIKSYKIAY 250
    SNDGKTWAMY KVKGTNEDMV FRGNIDNNTP YANSFTPPIK AQYVRLYPQV 300
    CRRHCTLRME LLGCELSGCS EPLGMKSGHI QDYQITASSI FRTLNMDMFT 350
    WEPRKARLDK QGKVNAWTSG HNDQSQWLQV DLLVPTKVTG IITQGAKDFG 400
    HVQFVGSYKL AYSNDGEHWT VYQDEKQRKD KVFQGNFDND THRKNVIDPP 450
    IYARHIRILP WSWYGRITLR SELLGCTEEE 480
    Length:480
    Mass (Da):53,765
    Last modified:June 1, 1998 - v1
    Checksum:iF7171E23A309FD48
    GO
    Isoform 2 (identifier: O43854-2) [UniParc]FASTAAdd to Basket

    Also known as: Short, Z20

    The sequence of this isoform differs from the canonical sequence as follows:
         66-66: A → G
         67-76: Missing.

    Show »
    Length:470
    Mass (Da):52,748
    Checksum:iEFF139A13FE5337A
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti16 – 161G → S in AAH30828. (PubMed:15489334)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei66 – 661A → G in isoform 2. 2 PublicationsVSP_050006
    Alternative sequencei67 – 7610Missing in isoform 2. 2 PublicationsVSP_050007

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U70312 mRNA. Translation: AAC02648.1.
    U70313 mRNA. Translation: AAC02649.1.
    AK312858 mRNA. Translation: BAG35710.1.
    CH471084 Genomic DNA. Translation: EAW95917.1.
    CH471084 Genomic DNA. Translation: EAW95918.1.
    BC030828 mRNA. Translation: AAH30828.1.
    BC053656 mRNA. Translation: AAH53656.1.
    CCDSiCCDS4062.1. [O43854-1]
    CCDS64195.1. [O43854-2]
    RefSeqiNP_001265571.1. NM_001278642.1. [O43854-2]
    NP_005702.3. NM_005711.4. [O43854-1]
    UniGeneiHs.482730.

    Genome annotation databases

    EnsembliENST00000296591; ENSP00000296591; ENSG00000164176. [O43854-1]
    ENST00000380138; ENSP00000369483; ENSG00000164176. [O43854-2]
    GeneIDi10085.
    KEGGihsa:10085.
    UCSCiuc003kio.1. human. [O43854-1]
    uc003kip.1. human. [O43854-2]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U70312 mRNA. Translation: AAC02648.1 .
    U70313 mRNA. Translation: AAC02649.1 .
    AK312858 mRNA. Translation: BAG35710.1 .
    CH471084 Genomic DNA. Translation: EAW95917.1 .
    CH471084 Genomic DNA. Translation: EAW95918.1 .
    BC030828 mRNA. Translation: AAH30828.1 .
    BC053656 mRNA. Translation: AAH53656.1 .
    CCDSi CCDS4062.1. [O43854-1 ]
    CCDS64195.1. [O43854-2 ]
    RefSeqi NP_001265571.1. NM_001278642.1. [O43854-2 ]
    NP_005702.3. NM_005711.4. [O43854-1 ]
    UniGenei Hs.482730.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4D90 X-ray 2.60 A/B 24-157 [» ]
    ProteinModelPortali O43854.
    SMRi O43854. Positions 26-480.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 115394. 3 interactions.
    IntActi O43854. 2 interactions.
    STRINGi 9606.ENSP00000296591.

    PTM databases

    PhosphoSitei O43854.

    Proteomic databases

    MaxQBi O43854.
    PaxDbi O43854.
    PRIDEi O43854.

    Protocols and materials databases

    DNASUi 10085.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000296591 ; ENSP00000296591 ; ENSG00000164176 . [O43854-1 ]
    ENST00000380138 ; ENSP00000369483 ; ENSG00000164176 . [O43854-2 ]
    GeneIDi 10085.
    KEGGi hsa:10085.
    UCSCi uc003kio.1. human. [O43854-1 ]
    uc003kip.1. human. [O43854-2 ]

    Organism-specific databases

    CTDi 10085.
    GeneCardsi GC05M083236.
    HGNCi HGNC:3173. EDIL3.
    HPAi HPA020415.
    MIMi 606018. gene.
    neXtProti NX_O43854.
    PharmGKBi PA27613.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG151278.
    HOGENOMi HOG000236278.
    HOVERGENi HBG002385.
    InParanoidi O43854.
    OMAi NINECEA.
    OrthoDBi EOG7ZWD1D.
    PhylomeDBi O43854.
    TreeFami TF330156.

    Miscellaneous databases

    GenomeRNAii 10085.
    NextBioi 38137.
    PROi O43854.
    SOURCEi Search...

    Gene expression databases

    Bgeei O43854.
    CleanExi HS_EDIL3.
    Genevestigatori O43854.

    Family and domain databases

    Gene3Di 2.60.120.260. 2 hits.
    InterProi IPR000421. Coagulation_fac_5/8-C_type_dom.
    IPR000742. EG-like_dom.
    IPR001881. EGF-like_Ca-bd_dom.
    IPR013032. EGF-like_CS.
    IPR000152. EGF-type_Asp/Asn_hydroxyl_site.
    IPR018097. EGF_Ca-bd_CS.
    IPR008979. Galactose-bd-like.
    [Graphical view ]
    Pfami PF00008. EGF. 2 hits.
    PF00754. F5_F8_type_C. 2 hits.
    [Graphical view ]
    SMARTi SM00181. EGF. 2 hits.
    SM00179. EGF_CA. 1 hit.
    SM00231. FA58C. 2 hits.
    [Graphical view ]
    SUPFAMi SSF49785. SSF49785. 2 hits.
    PROSITEi PS00010. ASX_HYDROXYL. 1 hit.
    PS00022. EGF_1. 2 hits.
    PS01186. EGF_2. 2 hits.
    PS50026. EGF_3. 3 hits.
    PS01187. EGF_CA. 1 hit.
    PS01285. FA58C_1. 2 hits.
    PS01286. FA58C_2. 2 hits.
    PS50022. FA58C_3. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning and characterization of developmental endothelial locus-1: an embryonic endothelial cell protein that binds the alphavbeta3 integrin receptor."
      Hidai C., Zupancic T.J., Penta K., Mikhail A., Kawana M., Quertermous E.E., Aoka Y., Fukagawa M., Matsui Y., Platika D., Auerbach R., Hogan B.L.M., Snodgrass R., Quertermous T.
      Genes Dev. 12:21-33(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), CHARACTERIZATION.
      Tissue: Embryonic lung.
    2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
      Tissue: Trachea.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
      Tissue: Brain.
    5. "The RGD finger of Del-1 is a unique structural feature critical for integrin binding."
      Schurpf T., Chen Q., Liu J.H., Wang R., Springer T.A., Wang J.H.
      FASEB J. 26:3412-3420(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 24-157, RGD MOTIF, DISULFIDE BONDS, CALCIUM-BINDING SITES, GLYCOSYLATION AT THR-73; THR-88 AND ASN-140.

    Entry informationi

    Entry nameiEDIL3_HUMAN
    AccessioniPrimary (citable) accession number: O43854
    Secondary accession number(s): B2R763
    , O43855, Q5D094, Q8N610
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 16, 2004
    Last sequence update: June 1, 1998
    Last modified: October 1, 2014
    This is version 122 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 5
      Human chromosome 5: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3