LSM4_HUMAN
ID LSM4_HUMAN Reviewed; 139 AA.
AC Q9Y4Z0;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 188.
DE RecName: Full=U6 snRNA-associated Sm-like protein LSm4;
DE AltName: Full=Glycine-rich protein;
DE Short=GRP;
GN Name=LSM4;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Liver;
RX PubMed=10369684; DOI=10.1093/emboj/18.12.3451;
RA Salgado-Garrido J., Bragado-Nilsson E., Kandels-Lewis S., Seraphin B.;
RT "Sm and Sm-like proteins assemble in two related complexes of deep
RT evolutionary origin.";
RL EMBO J. 18:3451-3462(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE, SUBUNIT, FUNCTION,
RP AND SUBCELLULAR LOCATION.
RX PubMed=10523320; DOI=10.1093/emboj/18.20.5789;
RA Achsel T., Brahms H., Kastner B., Bachi A., Wilm M., Luehrmann R.;
RT "A doughnut-shaped heteromer of human Sm-like proteins binds to the 3'-end
RT of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro.";
RL EMBO J. 18:5789-5802(1999).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Hypothalamus;
RX PubMed=10931946; DOI=10.1073/pnas.160270997;
RA Hu R.-M., Han Z.-G., Song H.-D., Peng Y.-D., Huang Q.-H., Ren S.-X.,
RA Gu Y.-J., Huang C.-H., Li Y.-B., Jiang C.-L., Fu G., Zhang Q.-H., Gu B.-W.,
RA Dai M., Mao Y.-F., Gao G.-F., Rong R., Ye M., Zhou J., Xu S.-H., Gu J.,
RA Shi J.-X., Jin W.-R., Zhang C.-K., Wu T.-M., Huang G.-Y., Chen Z.,
RA Chen M.-D., Chen J.-L.;
RT "Gene expression profiling in the human hypothalamus-pituitary-adrenal axis
RT and full-length cDNA cloning.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:9543-9548(2000).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Chan E.K.L.;
RL Submitted (APR-2000) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Lung;
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 [6]
RP PROTEIN SEQUENCE OF 1-20, ACETYLATION AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC TISSUE=Mammary carcinoma;
RA Bienvenut W.V., Matallanas D., Cooper W.N., Kolch W.;
RL Submitted (JUL-2007) to UniProtKB.
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
RA Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L.,
RA Ye M., Zou H.;
RT "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver
RT phosphoproteome.";
RL J. Proteomics 96:253-262(2014).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=25944712; DOI=10.1002/pmic.201400617;
RA Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M., Ayoub D.,
RA Lane L., Bairoch A., Van Dorsselaer A., Carapito C.;
RT "N-terminome analysis of the human mitochondrial proteome.";
RL Proteomics 15:2519-2524(2015).
RN [10]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-80, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=28112733; DOI=10.1038/nsmb.3366;
RA Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
RA Nielsen M.L.;
RT "Site-specific mapping of the human SUMO proteome reveals co-modification
RT with phosphorylation.";
RL Nat. Struct. Mol. Biol. 24:325-336(2017).
RN [11] {ECO:0007744|PDB:3JCR}
RP STRUCTURE BY ELECTRON MICROSCOPY (7.00 ANGSTROMS), SUBCELLULAR LOCATION,
RP SUBUNIT, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=26912367; DOI=10.1126/science.aad2085;
RA Agafonov D.E., Kastner B., Dybkov O., Hofele R.V., Liu W.T., Urlaub H.,
RA Luhrmann R., Stark H.;
RT "Molecular architecture of the human U4/U6.U5 tri-snRNP.";
RL Science 351:1416-1420(2016).
RN [12] {ECO:0007744|PDB:5O9Z}
RP STRUCTURE BY ELECTRON MICROSCOPY (4.50 ANGSTROMS), FUNCTION, SUBCELLULAR
RP LOCATION, SUBUNIT, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=28781166; DOI=10.1016/j.cell.2017.07.011;
RA Bertram K., Agafonov D.E., Dybkov O., Haselbach D., Leelaram M.N.,
RA Will C.L., Urlaub H., Kastner B., Luhrmann R., Stark H.;
RT "Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for
RT Activation.";
RL Cell 170:701-713(2017).
CC -!- FUNCTION: Plays role in pre-mRNA splicing as component of the U4/U6-U5
CC tri-snRNP complex that is involved in spliceosome assembly, and as
CC component of the precatalytic spliceosome (spliceosome B complex)
CC (PubMed:28781166). The heptameric LSM2-8 complex binds specifically to
CC the 3'-terminal U-tract of U6 snRNA (PubMed:10523320).
CC {ECO:0000269|PubMed:10523320, ECO:0000269|PubMed:28781166}.
CC -!- SUBUNIT: Component of the precatalytic spliceosome (spliceosome B
CC complex) (PubMed:28781166). Component of the U4/U6-U5 tri-snRNP
CC complex, a building block of the precatalytic spliceosome (spliceosome
CC B complex) (PubMed:10523320, PubMed:28781166, PubMed:26912367). The
CC U4/U6-U5 tri-snRNP complex is composed of the U4, U6 and U5 snRNAs and
CC at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40,
CC SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2,
CC PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5,
CC LSM6, LSM7 and LSM8 (PubMed:26912367). LSM2, LSM3, LSM4, LSM5, LSM6,
CC LSM7 and LSM8 form a heptameric, ring-shaped subcomplex (the LSM2-8
CC complex) that is part of the U4/U6-U5 tri-snRNP complex and the
CC precatalytic spliceosome (PubMed:10523320, PubMed:26912367,
CC PubMed:28781166). {ECO:0000269|PubMed:10523320,
CC ECO:0000269|PubMed:26912367, ECO:0000269|PubMed:28781166}.
CC -!- INTERACTION:
CC Q9Y4Z0; Q13137: CALCOCO2; NbExp=7; IntAct=EBI-372521, EBI-739580;
CC Q9Y4Z0; Q96B26: EXOSC8; NbExp=3; IntAct=EBI-372521, EBI-371922;
CC Q9Y4Z0; O60861-1: GAS7; NbExp=3; IntAct=EBI-372521, EBI-11745923;
CC Q9Y4Z0; Q13422: IKZF1; NbExp=3; IntAct=EBI-372521, EBI-745305;
CC Q9Y4Z0; Q96JM7: L3MBTL3; NbExp=3; IntAct=EBI-372521, EBI-2686809;
CC Q9Y4Z0; O15116: LSM1; NbExp=4; IntAct=EBI-372521, EBI-347619;
CC Q9Y4Z0; Q9UK45: LSM7; NbExp=11; IntAct=EBI-372521, EBI-348372;
CC Q9Y4Z0; O95777: LSM8; NbExp=4; IntAct=EBI-372521, EBI-347779;
CC Q9Y4Z0; O43586: PSTPIP1; NbExp=6; IntAct=EBI-372521, EBI-1050964;
CC Q9Y4Z0; Q96DT7: ZBTB10; NbExp=3; IntAct=EBI-372521, EBI-10235384;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:10523320,
CC ECO:0000269|PubMed:26912367, ECO:0000269|PubMed:28781166}.
CC -!- SIMILARITY: Belongs to the snRNP Sm proteins family. {ECO:0000305}.
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DR EMBL; AJ238096; CAB45867.1; -; mRNA.
DR EMBL; AF182290; AAD56228.1; -; mRNA.
DR EMBL; AF117235; AAF17216.1; -; mRNA.
DR EMBL; AF251218; AAF90055.1; -; mRNA.
DR EMBL; BC000387; AAH00387.1; -; mRNA.
DR EMBL; BC003652; AAH03652.1; -; mRNA.
DR EMBL; BC022198; AAH22198.1; -; mRNA.
DR EMBL; BC023665; AAH23665.1; -; mRNA.
DR CCDS; CCDS12374.1; -.
DR RefSeq; NP_036453.1; NM_012321.4.
DR PDB; 3JCR; EM; 7.00 A; 4=1-139.
DR PDB; 5O9Z; EM; 4.50 A; q=1-139.
DR PDB; 6AH0; EM; 5.70 A; s=1-139.
DR PDB; 6AHD; EM; 3.80 A; s=1-139.
DR PDB; 6QW6; EM; 2.92 A; 64=1-139.
DR PDB; 6QX9; EM; 3.28 A; 64=1-139.
DR PDB; 7ABG; EM; 7.80 A; C=1-139.
DR PDBsum; 3JCR; -.
DR PDBsum; 5O9Z; -.
DR PDBsum; 6AH0; -.
DR PDBsum; 6AHD; -.
DR PDBsum; 6QW6; -.
DR PDBsum; 6QX9; -.
DR PDBsum; 7ABG; -.
DR AlphaFoldDB; Q9Y4Z0; -.
DR SMR; Q9Y4Z0; -.
DR BioGRID; 117336; 142.
DR ComplexPortal; CPX-2391; U4/U6.U5 small nuclear ribonucleoprotein complex.
DR CORUM; Q9Y4Z0; -.
DR DIP; DIP-31209N; -.
DR IntAct; Q9Y4Z0; 39.
DR MINT; Q9Y4Z0; -.
DR STRING; 9606.ENSP00000469468; -.
DR iPTMnet; Q9Y4Z0; -.
DR MetOSite; Q9Y4Z0; -.
DR PhosphoSitePlus; Q9Y4Z0; -.
DR SwissPalm; Q9Y4Z0; -.
DR BioMuta; LSM4; -.
DR DMDM; 10720082; -.
DR EPD; Q9Y4Z0; -.
DR jPOST; Q9Y4Z0; -.
DR MassIVE; Q9Y4Z0; -.
DR MaxQB; Q9Y4Z0; -.
DR PaxDb; Q9Y4Z0; -.
DR PeptideAtlas; Q9Y4Z0; -.
DR PRIDE; Q9Y4Z0; -.
DR ProteomicsDB; 86267; -.
DR Antibodypedia; 28019; 219 antibodies from 26 providers.
DR DNASU; 25804; -.
DR Ensembl; ENST00000593829.6; ENSP00000469468.2; ENSG00000130520.11.
DR GeneID; 25804; -.
DR KEGG; hsa:25804; -.
DR MANE-Select; ENST00000593829.6; ENSP00000469468.2; NM_012321.5; NP_036453.1.
DR UCSC; uc002niq.4; human.
DR CTD; 25804; -.
DR DisGeNET; 25804; -.
DR GeneCards; LSM4; -.
DR HGNC; HGNC:17259; LSM4.
DR HPA; ENSG00000130520; Low tissue specificity.
DR MIM; 607284; gene.
DR neXtProt; NX_Q9Y4Z0; -.
DR OpenTargets; ENSG00000130520; -.
DR PharmGKB; PA134906569; -.
DR VEuPathDB; HostDB:ENSG00000130520; -.
DR eggNOG; KOG3293; Eukaryota.
DR GeneTree; ENSGT00610000086173; -.
DR HOGENOM; CLU_099537_2_1_1; -.
DR InParanoid; Q9Y4Z0; -.
DR OMA; VACDAWM; -.
DR OrthoDB; 1571169at2759; -.
DR PhylomeDB; Q9Y4Z0; -.
DR TreeFam; TF315027; -.
DR PathwayCommons; Q9Y4Z0; -.
DR Reactome; R-HSA-430039; mRNA decay by 5' to 3' exoribonuclease.
DR Reactome; R-HSA-72163; mRNA Splicing - Major Pathway.
DR SignaLink; Q9Y4Z0; -.
DR BioGRID-ORCS; 25804; 774 hits in 1082 CRISPR screens.
DR ChiTaRS; LSM4; human.
DR GeneWiki; LSM4; -.
DR GenomeRNAi; 25804; -.
DR Pharos; Q9Y4Z0; Tbio.
DR PRO; PR:Q9Y4Z0; -.
DR Proteomes; UP000005640; Chromosome 19.
DR RNAct; Q9Y4Z0; protein.
DR Bgee; ENSG00000130520; Expressed in mucosa of transverse colon and 207 other tissues.
DR ExpressionAtlas; Q9Y4Z0; baseline and differential.
DR Genevisible; Q9Y4Z0; HS.
DR GO; GO:0005829; C:cytosol; IDA:CAFA.
DR GO; GO:0120115; C:Lsm2-8 complex; IDA:UniProtKB.
DR GO; GO:0016020; C:membrane; IDA:CAFA.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0000932; C:P-body; IBA:GO_Central.
DR GO; GO:0032991; C:protein-containing complex; IDA:CAFA.
DR GO; GO:0097526; C:spliceosomal tri-snRNP complex; IBA:GO_Central.
DR GO; GO:0071005; C:U2-type precatalytic spliceosome; IDA:UniProtKB.
DR GO; GO:0046540; C:U4/U6 x U5 tri-snRNP complex; IDA:UniProtKB.
DR GO; GO:0005688; C:U6 snRNP; IBA:GO_Central.
DR GO; GO:0042731; F:PH domain binding; IDA:CAFA.
DR GO; GO:0003723; F:RNA binding; HDA:UniProtKB.
DR GO; GO:0017070; F:U6 snRNA binding; IBA:GO_Central.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IDA:UniProtKB.
DR GO; GO:0000956; P:nuclear-transcribed mRNA catabolic process; IEA:InterPro.
DR GO; GO:0033962; P:P-body assembly; IBA:GO_Central.
DR GO; GO:0008380; P:RNA splicing; TAS:ProtInc.
DR GO; GO:0000387; P:spliceosomal snRNP assembly; IBA:GO_Central.
DR CDD; cd01723; LSm4; 1.
DR InterPro; IPR034101; Lsm4.
DR InterPro; IPR027141; LSm4/Sm_D1/D3.
DR InterPro; IPR001163; LSM_dom_euk/arc.
DR InterPro; IPR010920; LSM_dom_sf.
DR PANTHER; PTHR23338; PTHR23338; 1.
DR Pfam; PF01423; LSM; 1.
DR SMART; SM00651; Sm; 1.
DR SUPFAM; SSF50182; SSF50182; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Direct protein sequencing; Isopeptide bond;
KW mRNA processing; mRNA splicing; Nucleus; Reference proteome;
KW Ribonucleoprotein; RNA-binding; Spliceosome; Ubl conjugation.
FT CHAIN 1..139
FT /note="U6 snRNA-associated Sm-like protein LSm4"
FT /id="PRO_0000125564"
FT REGION 87..139
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0000269|Ref.6"
FT CROSSLNK 80
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
SQ SEQUENCE 139 AA; 15350 MW; BCEFB20247335A1B CRC64;
MLPLSLLKTA QNHPMLVELK NGETYNGHLV SCDNWMNINL REVICTSRDG DKFWRMPECY
IRGSTIKYLR IPDEIIDMVK EEVVAKGRGR GGLQQQKQQK GRGMGGAGRG VFGGRGRGGI
PGTGRGQPEK KPGRQAGKQ
