RL4_MOUSE
ID RL4_MOUSE Reviewed; 419 AA.
AC Q9D8E6; Q9CY08;
DT 26-JUL-2002, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 175.
DE RecName: Full=60S ribosomal protein L4;
GN Name=Rpl4;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J; TISSUE=Embryonic liver, and Small intestine;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP PROTEIN SEQUENCE OF 2-13; 165-171 AND 353-363, CLEAVAGE OF INITIATOR
RP METHIONINE, ACETYLATION AT ALA-2, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=C57BL/6J; TISSUE=Skeletal muscle;
RA Kanor S., Quadroni M., Bienvenut W.V.;
RL Submitted (MAR-2006) to UniProtKB.
RN [4]
RP INTERACTION WITH IPO9.
RX PubMed=11823430; DOI=10.1093/emboj/21.3.377;
RA Jaekel S., Mingot J.-M., Schwarzmaier P., Hartmann E., Goerlich D.;
RT "Importins fulfill a dual function as nuclear import receptors and
RT cytoplasmic chaperones for exposed basic domains.";
RL EMBO J. 21:377-386(2002).
RN [5]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-295, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Embryonic fibroblast;
RX PubMed=19131326; DOI=10.1074/mcp.m800451-mcp200;
RA Sweet S.M., Bailey C.M., Cunningham D.L., Heath J.K., Cooper H.J.;
RT "Large scale localization of protein phosphorylation by use of electron
RT capture dissociation mass spectrometry.";
RL Mol. Cell. Proteomics 8:904-912(2009).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas,
RC Spleen, and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
RN [7]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-259; LYS-353 AND LYS-364, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Embryonic fibroblast;
RX PubMed=23806337; DOI=10.1016/j.molcel.2013.06.001;
RA Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y.,
RA Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.;
RT "SIRT5-mediated lysine desuccinylation impacts diverse metabolic
RT pathways.";
RL Mol. Cell 50:919-930(2013).
RN [8]
RP METHYLATION [LARGE SCALE ANALYSIS] AT ARG-97, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, and Embryo;
RX PubMed=24129315; DOI=10.1074/mcp.o113.027870;
RA Guo A., Gu H., Zhou J., Mulhern D., Wang Y., Lee K.A., Yang V., Aguiar M.,
RA Kornhauser J., Jia X., Ren J., Beausoleil S.A., Silva J.C., Vemulapalli V.,
RA Bedford M.T., Comb M.J.;
RT "Immunoaffinity enrichment and mass spectrometry analysis of protein
RT methylation.";
RL Mol. Cell. Proteomics 13:372-387(2014).
RN [9]
RP CITRULLINATION AT ARG-300.
RX PubMed=24463520; DOI=10.1038/nature12942;
RA Christophorou M.A., Castelo-Branco G., Halley-Stott R.P., Oliveira C.S.,
RA Loos R., Radzisheuskaya A., Mowen K.A., Bertone P., Silva J.C.,
RA Zernicka-Goetz M., Nielsen M.L., Gurdon J.B., Kouzarides T.;
RT "Citrullination regulates pluripotency and histone H1 binding to
RT chromatin.";
RL Nature 507:104-108(2014).
CC -!- FUNCTION: Component of the large ribosomal subunit. The ribosome is a
CC large ribonucleoprotein complex responsible for the synthesis of
CC proteins in the cell. {ECO:0000250|UniProtKB:P36578}.
CC -!- SUBUNIT: Component of the large ribosomal subunit. May bind IPO9 with
CC low affinity (By similarity). Interacts with RBM3 (By similarity).
CC {ECO:0000250|UniProtKB:P36578, ECO:0000250|UniProtKB:P50878}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P36578}.
CC -!- PTM: Citrullinated by PADI4. {ECO:0000269|PubMed:24463520}.
CC -!- SIMILARITY: Belongs to the universal ribosomal protein uL4 family.
CC {ECO:0000305}.
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DR EMBL; AK008098; BAB25458.1; -; mRNA.
DR EMBL; AK011068; BAB27375.1; -; mRNA.
DR EMBL; BC003459; AAH03459.1; -; mRNA.
DR CCDS; CCDS40667.1; -.
DR RefSeq; NP_077174.1; NM_024212.4.
DR PDB; 6SWA; EM; 3.10 A; C=1-419.
DR PDB; 7CPU; EM; 2.82 A; LC=1-419.
DR PDB; 7CPV; EM; 3.03 A; LC=1-419.
DR PDB; 7LS1; EM; 3.30 A; F2=1-419.
DR PDB; 7LS2; EM; 3.10 A; F2=1-419.
DR PDBsum; 6SWA; -.
DR PDBsum; 7CPU; -.
DR PDBsum; 7CPV; -.
DR PDBsum; 7LS1; -.
DR PDBsum; 7LS2; -.
DR AlphaFoldDB; Q9D8E6; -.
DR SMR; Q9D8E6; -.
DR BioGRID; 212515; 106.
DR ComplexPortal; CPX-5262; 60S cytosolic large ribosomal subunit.
DR CORUM; Q9D8E6; -.
DR IntAct; Q9D8E6; 4.
DR MINT; Q9D8E6; -.
DR STRING; 10090.ENSMUSP00000034966; -.
DR iPTMnet; Q9D8E6; -.
DR PhosphoSitePlus; Q9D8E6; -.
DR SwissPalm; Q9D8E6; -.
DR EPD; Q9D8E6; -.
DR jPOST; Q9D8E6; -.
DR MaxQB; Q9D8E6; -.
DR PaxDb; Q9D8E6; -.
DR PRIDE; Q9D8E6; -.
DR ProteomicsDB; 253305; -.
DR Antibodypedia; 26140; 175 antibodies from 29 providers.
DR DNASU; 67891; -.
DR Ensembl; ENSMUST00000034966; ENSMUSP00000034966; ENSMUSG00000032399.
DR GeneID; 67891; -.
DR KEGG; mmu:67891; -.
DR UCSC; uc009qbn.1; mouse.
DR CTD; 6124; -.
DR MGI; MGI:1915141; Rpl4.
DR VEuPathDB; HostDB:ENSMUSG00000032399; -.
DR eggNOG; KOG1475; Eukaryota.
DR GeneTree; ENSGT00390000018145; -.
DR HOGENOM; CLU_026535_4_0_1; -.
DR InParanoid; Q9D8E6; -.
DR OMA; WHQKVNV; -.
DR OrthoDB; 878848at2759; -.
DR PhylomeDB; Q9D8E6; -.
DR TreeFam; TF300593; -.
DR Reactome; R-MMU-156827; L13a-mediated translational silencing of Ceruloplasmin expression.
DR Reactome; R-MMU-1799339; SRP-dependent cotranslational protein targeting to membrane.
DR Reactome; R-MMU-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR Reactome; R-MMU-72689; Formation of a pool of free 40S subunits.
DR Reactome; R-MMU-72706; GTP hydrolysis and joining of the 60S ribosomal subunit.
DR Reactome; R-MMU-975956; Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
DR Reactome; R-MMU-975957; Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
DR BioGRID-ORCS; 67891; 30 hits in 67 CRISPR screens.
DR ChiTaRS; Rpl4; mouse.
DR PRO; PR:Q9D8E6; -.
DR Proteomes; UP000000589; Chromosome 9.
DR RNAct; Q9D8E6; protein.
DR Bgee; ENSMUSG00000032399; Expressed in embryonic post-anal tail and 63 other tissues.
DR ExpressionAtlas; Q9D8E6; baseline and differential.
DR Genevisible; Q9D8E6; MM.
DR GO; GO:0031672; C:A band; ISO:MGI.
DR GO; GO:0005737; C:cytoplasm; IC:ComplexPortal.
DR GO; GO:0005829; C:cytosol; TAS:Reactome.
DR GO; GO:0022625; C:cytosolic large ribosomal subunit; IPI:ComplexPortal.
DR GO; GO:0022626; C:cytosolic ribosome; ISO:MGI.
DR GO; GO:0015934; C:large ribosomal subunit; ISO:MGI.
DR GO; GO:0005634; C:nucleus; ISO:MGI.
DR GO; GO:0014069; C:postsynaptic density; ISO:MGI.
DR GO; GO:1990904; C:ribonucleoprotein complex; ISO:MGI.
DR GO; GO:0005791; C:rough endoplasmic reticulum; ISO:MGI.
DR GO; GO:0008097; F:5S rRNA binding; ISO:MGI.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0003735; F:structural constituent of ribosome; ISO:MGI.
DR GO; GO:0002181; P:cytoplasmic translation; IC:ComplexPortal.
DR GO; GO:0045773; P:positive regulation of axon extension; ISO:MGI.
DR GO; GO:0050772; P:positive regulation of axonogenesis; ISO:MGI.
DR Gene3D; 3.40.1370.10; -; 1.
DR InterPro; IPR025755; Ribos_L4_C_dom.
DR InterPro; IPR002136; Ribosomal_L4/L1e.
DR InterPro; IPR013000; Ribosomal_L4/L1e_euk/arc_CS.
DR InterPro; IPR023574; Ribosomal_L4_dom_sf.
DR InterPro; IPR045240; Ribosomal_L4_euk/arch.
DR PANTHER; PTHR19431; PTHR19431; 1.
DR Pfam; PF14374; Ribos_L4_asso_C; 1.
DR Pfam; PF00573; Ribosomal_L4; 1.
DR SUPFAM; SSF52166; SSF52166; 1.
DR PROSITE; PS00939; RIBOSOMAL_L1E; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Citrullination; Cytoplasm;
KW Direct protein sequencing; Isopeptide bond; Methylation; Phosphoprotein;
KW Reference proteome; Ribonucleoprotein; Ribosomal protein; Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|Ref.3"
FT CHAIN 2..419
FT /note="60S ribosomal protein L4"
FT /id="PRO_0000129351"
FT REGION 364..419
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 369..383
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 394..419
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0000269|Ref.3"
FT MOD_RES 14
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P36578"
FT MOD_RES 97
FT /note="Omega-N-methylarginine"
FT /evidence="ECO:0007744|PubMed:24129315"
FT MOD_RES 106
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P36578"
FT MOD_RES 259
FT /note="N6-acetyllysine"
FT /evidence="ECO:0007744|PubMed:23806337"
FT MOD_RES 266
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:P36578"
FT MOD_RES 290
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P50878"
FT MOD_RES 295
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19131326"
FT MOD_RES 300
FT /note="Citrulline"
FT /evidence="ECO:0000269|PubMed:24463520"
FT MOD_RES 333
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P36578"
FT MOD_RES 353
FT /note="N6-acetyllysine"
FT /evidence="ECO:0007744|PubMed:23806337"
FT MOD_RES 364
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0007744|PubMed:23806337"
FT MOD_RES 365
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P36578"
FT CROSSLNK 239
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P36578"
FT CROSSLNK 327
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P36578"
FT CROSSLNK 364
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO1); alternate"
FT /evidence="ECO:0000250|UniProtKB:P36578"
FT CONFLICT 161
FT /note="Y -> F (in Ref. 1; BAB27375)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 419 AA; 47154 MW; E736E656A60BE85B CRC64;
MACARPLISV YSEKGESSGK NVTLPAVFKA PIRPDIVNFV HTNLRKNNRQ PYAVSELAGH
QTSAESWGTG RAVARIPRVR GGGTHRSGQG AFGNMCRGGR MFAPTKTWRR WHRRVNTTQK
RYAICSALAA SALPALVMSK GHRIEEVPEL PLVVEDKVEG YKKTKEAVQL LKKLKAWNDI
KKVYASQRMR AGKGKMRNRR RIQRRGPCII YNEDNGIIKA FRNIPGITLL NVSKLNILKL
APGGHVGRFC IWTESAFRKL DELYGTWRKA ASLKSNYNLP MHKMMNTDLS RILKSPEIQR
ALRAPRKKIH RRVLKKNPLK NLRIMLKLNP YAKTMRRNTI LRQARNHKLR VKKLEAAATA
LATKSEKVVP EKGTADKKPA VGKKGKKVDA KKQKPAGKKV VAKKPAEKKP TTEEKKPAA
