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Protein

Interleukin enhancer-binding factor 3

Gene

Ilf3

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

Functioni

RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Within the nucleus, promotes circRNAs processing by stabilizing the regulatory elements residing in the flanking introns of the circularized exons. Plays thereby a role in the back-splicing of a subset of circRNAs. As a consequence, participates in a wide range of transcriptional and post-transcriptional processes. Upon viral infection, ILF3 accumulates in the cytoplasm and participates in the innate antiviral response. Mechanistically, ILF3 becomes phosphorylated and activated by the double-stranded RNA-activated protein kinase/PKR which releases ILF3 from cellular mature circRNAs. In turn, unbound ILF3 molecules are able to interact with and thus inhibit viral mRNAs.By similarity

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • double-stranded RNA binding Source: InterPro
  • enzyme binding Source: RGD
  • transcription factor activity, sequence-specific DNA binding Source: RGD

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, RNA-binding
Biological processAntiviral defense, Transcription, Transcription regulation

Names & Taxonomyi

Protein namesi
Recommended name:
Interleukin enhancer-binding factor 3
Gene namesi
Name:Ilf3
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi619734. Ilf3.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001260721 – 897Interleukin enhancer-binding factor 3Add BLAST897

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei67PhosphothreonineCombined sources1
Modified residuei100N6-acetyllysineBy similarity1
Modified residuei188Phosphothreonine; by PKRBy similarity1
Modified residuei190PhosphoserineBy similarity1
Modified residuei315Phosphothreonine; by PKRBy similarity1
Cross-linki348Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1)By similarity
Modified residuei382PhosphoserineCombined sources1
Modified residuei384PhosphoserineBy similarity1
Cross-linki396Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei460N6-acetyllysineBy similarity1
Modified residuei476PhosphoserineCombined sources1
Modified residuei477PhosphoserineCombined sources1
Modified residuei482PhosphoserineCombined sources1
Modified residuei486PhosphoserineCombined sources1
Cross-linki489Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei609Omega-N-methylated arginineBy similarity1
Modified residuei794PhosphoserineBy similarity1
Modified residuei812PhosphoserineBy similarity1
Modified residuei814PhosphoserineBy similarity1
Modified residuei818PhosphoserineBy similarity1

Post-translational modificationi

Phosphorylated at Thr-188 and Thr-315 by PKR in response to RNA viruses. This phosphorylation results in the dissociation of ILF2 from the ILF2-ILF3 complex resulting in a cytoplasmic sequestration of ILF3 where it can bind to viral RNAs and impede viral replication.By similarity
Methylated by protein arginine N-methyltransferase 1.By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ9JIL3.
PRIDEiQ9JIL3.

PTM databases

iPTMnetiQ9JIL3.
PhosphoSitePlusiQ9JIL3.

Interactioni

Subunit structurei

Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs. Interacts with FUS and SMN. Interacts (via C-terminus) with PRMT1. Forms a complex with ILF2. Can also bind to PRKDC/XRCC7: this may stabilize the interaction of PRKDC/XRCC7 and the heterodimeric complex of XRCC6/KU70 and XRCC5/KU80. Forms a heteromeric complex with ZNF346 and ILF3. Found in a nuclear export complex with XPO5, ILF3, Ran and double-stranded RNA or double-stranded minihelix VA1 RNA. Found in a nuclear export complex with XPO5, RAN, ILF3, ZNF346 and double-stranded RNA. Interacts with XPO5 and ZNF346. Forms a complex with ILF2, YLPM1, KHDRBS1, RBMX, NCOA5 and PPP1CA. Interacts with AGO1 and AGO2.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
Prmt1Q630092EBI-78714,EBI-78708

GO - Molecular functioni

  • enzyme binding Source: RGD

Protein-protein interaction databases

BioGridi249972. 1 interactor.
IntActiQ9JIL3. 2 interactors.
STRINGi10116.ENSRNOP00000009354.

Structurei

3D structure databases

ProteinModelPortaliQ9JIL3.
SMRiQ9JIL3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini5 – 378DZFPROSITE-ProRule annotationAdd BLAST374
Domaini398 – 467DRBM 1PROSITE-ProRule annotationAdd BLAST70
Domaini524 – 590DRBM 2PROSITE-ProRule annotationAdd BLAST67

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni609 – 897Interaction with PRMT1Add BLAST289

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi371 – 389Bipartite nuclear localization signalSequence analysisAdd BLAST19

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi385 – 389Poly-Lys5
Compositional biasi634 – 637Poly-Pro4
Compositional biasi640 – 659Arg/Gly-richAdd BLAST20
Compositional biasi701 – 710Poly-Gly10
Compositional biasi796 – 800Poly-Gly5

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG3792. Eukaryota.
ENOG410XPBY. LUCA.
HOGENOMiHOG000232164.
HOVERGENiHBG069915.
InParanoidiQ9JIL3.
KOiK13090.
PhylomeDBiQ9JIL3.

Family and domain databases

InterProiView protein in InterPro
IPR014720. dsRBD_dom.
IPR006561. DZF_dom.
IPR033099. ILF3/NF90.
PANTHERiPTHR10910:SF34. PTHR10910:SF34. 1 hit.
PfamiView protein in Pfam
PF00035. dsrm. 2 hits.
PF07528. DZF. 1 hit.
SMARTiView protein in SMART
SM00358. DSRM. 2 hits.
SM00572. DZF. 1 hit.
PROSITEiView protein in PROSITE
PS50137. DS_RBD. 2 hits.
PS51703. DZF. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9JIL3-1) [UniParc]FASTAAdd to basket

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

        10         20         30         40         50
MRPMRIFVND DRHVMAKHSS VYPTQEELEA VQNMVSHTER ALKAVSDWID
60 70 80 90 100
EQEKGNSELS EAENMDTPPD DESKEGAGEQ KAEHMTRTLR GVMRVGLVAK
110 120 130 140 150
GLLLKGDLDL ELVLLCKEKP TTALLDKVAD NLAIQLTTVT EDKYEILQSV
160 170 180 190 200
DDAAIVIKNT KEPPLSLTIH LTSPVVREEM EKVLAGETLS VNDPPDVLDR
210 220 230 240 250
QKCLAALASL RHAKWFQARA NGLKSCVIVI RVLRDLCTRV PTWGPLRGWP
260 270 280 290 300
LELLCEKSIG TANRPMGAGE ALRRVLECLA SGIVMPDGSG IYDPCEKEAT
310 320 330 340 350
DAIGHLDRQQ REDITQSAQH ALRLAAFGQL HKVLGMDPLP SKMPKKPKNE
360 370 380 390 400
NPVDYTVQIP PSTTYAITPM KRPMEEDGEE KSPSKKKKKI QKKEEKAEPP
410 420 430 440 450
QAMNALMRLN QLKPGLQYKL ISQTGPVHAP IFTMSVEVDG STFEASGPSK
460 470 480 490 500
KTAKLHVAVK VLQDMGLPTG AEGRDSSKGE DSAEESDGKP AVVAPPPVVE
510 520 530 540 550
AVSNPSSVFP SDATTEQGPI LTKHGKNPVM ELNEKRRGLK YELISETGGS
560 570 580 590 600
HDKRFVMEVE VDGQKFQGAG SNKKVAKAYA ALAALEKLFP DAPLALEANK
610 620 630 640 650
KKRAPVPVRG GPKFAAKPHN PGFGMGGPMH NEAPPPPNIR GRGRGGNIRG
660 670 680 690 700
RGRGRGFGGT NHGGGYMNAG AGYGSYGYSS NSATAGYSQF YSNGGHYGNA
710 720 730 740 750
GGGGSGGGGG SSSYSSYYQG DSYNSPVPPK HAGKKPLHGG QQKPSYSSGY
760 770 780 790 800
QSHQGQQQPY NQSQYSSYGT PQGKQKGYGH GQGSYSSYSN SYNSPGGGGG
810 820 830 840 850
SDYSYDSKFN YSGSGGRSGG NSYGSSGSSY NTGSHGGYGA GSGGSSSYQG
860 870 880 890
KQGGYSSQSN YSSPGSSQSY SGPASSYQSS QGGYSRNTEH SMNYQYR
Length:897
Mass (Da):95,935
Last modified:April 12, 2005 - v2
Checksum:iACD800D1858539BB
GO
Isoform 2 (identifier: Q9JIL3-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MALYHHHFITRRRR

Show »
Length:910
Mass (Da):97,680
Checksum:iD6AB97A4B52E442A
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0134091M → MALYHHHFITRRRR in isoform 2. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF220102 mRNA. Translation: AAF31446.1.
AABR03063190 Genomic DNA. No translation available.
AABR03065470 Genomic DNA. No translation available.
RefSeqiNP_445864.1. NM_053412.1. [Q9JIL3-2]
UniGeneiRn.203881.

Genome annotation databases

GeneIDi84472.
KEGGirno:84472.
UCSCiRGD:619734. rat. [Q9JIL3-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiILF3_RAT
AccessioniPrimary (citable) accession number: Q9JIL3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 31, 2002
Last sequence update: April 12, 2005
Last modified: October 25, 2017
This is version 126 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome