SMD3_HUMAN
ID SMD3_HUMAN Reviewed; 126 AA.
AC P62318; B4DJP7; B5BU13; P43331;
DT 05-JUL-2004, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 180.
DE RecName: Full=Small nuclear ribonucleoprotein Sm D3;
DE Short=Sm-D3;
DE AltName: Full=snRNP core protein D3;
GN Name=SNRPD3;
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] (ISOFORM 1), AND PARTIAL PROTEIN SEQUENCE.
RX PubMed=7527560; DOI=10.1073/pnas.91.25.12317;
RA Lehmeier T., Raker V., Hermann H., Luehrmann R.;
RT "cDNA cloning of the Sm proteins D2 and D3 from human small nuclear
RT ribonucleoproteins: evidence for a direct D1-D2 interaction.";
RL Proc. Natl. Acad. Sci. U.S.A. 91:12317-12321(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RX PubMed=15461802; DOI=10.1186/gb-2004-5-10-r84;
RA Collins J.E., Wright C.L., Edwards C.A., Davis M.P., Grinham J.A.,
RA Cole C.G., Goward M.E., Aguado B., Mallya M., Mokrab Y., Huckle E.J.,
RA Beare D.M., Dunham I.;
RT "A genome annotation-driven approach to cloning the human ORFeome.";
RL Genome Biol. 5:R84.1-R84.11(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Thalamus;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RX PubMed=19054851; DOI=10.1038/nmeth.1273;
RA Goshima N., Kawamura Y., Fukumoto A., Miura A., Honma R., Satoh R.,
RA Wakamatsu A., Yamamoto J., Kimura K., Nishikawa T., Andoh T., Iida Y.,
RA Ishikawa K., Ito E., Kagawa N., Kaminaga C., Kanehori K., Kawakami B.,
RA Kenmochi K., Kimura R., Kobayashi M., Kuroita T., Kuwayama H., Maruyama Y.,
RA Matsuo K., Minami K., Mitsubori M., Mori M., Morishita R., Murase A.,
RA Nishikawa A., Nishikawa S., Okamoto T., Sakagami N., Sakamoto Y.,
RA Sasaki Y., Seki T., Sono S., Sugiyama A., Sumiya T., Takayama T.,
RA Takayama Y., Takeda H., Togashi T., Yahata K., Yamada H., Yanagisawa Y.,
RA Endo Y., Imamoto F., Kisu Y., Tanaka S., Isogai T., Imai J., Watanabe S.,
RA Nomura N.;
RT "Human protein factory for converting the transcriptome into an in vitro-
RT expressed proteome.";
RL Nat. Methods 5:1011-1017(2008).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=10591208; DOI=10.1038/990031;
RA Dunham I., Hunt A.R., Collins J.E., Bruskiewich R., Beare D.M., Clamp M.,
RA Smink L.J., Ainscough R., Almeida J.P., Babbage A.K., Bagguley C.,
RA Bailey J., Barlow K.F., Bates K.N., Beasley O.P., Bird C.P., Blakey S.E.,
RA Bridgeman A.M., Buck D., Burgess J., Burrill W.D., Burton J., Carder C.,
RA Carter N.P., Chen Y., Clark G., Clegg S.M., Cobley V.E., Cole C.G.,
RA Collier R.E., Connor R., Conroy D., Corby N.R., Coville G.J., Cox A.V.,
RA Davis J., Dawson E., Dhami P.D., Dockree C., Dodsworth S.J., Durbin R.M.,
RA Ellington A.G., Evans K.L., Fey J.M., Fleming K., French L., Garner A.A.,
RA Gilbert J.G.R., Goward M.E., Grafham D.V., Griffiths M.N.D., Hall C.,
RA Hall R.E., Hall-Tamlyn G., Heathcott R.W., Ho S., Holmes S., Hunt S.E.,
RA Jones M.C., Kershaw J., Kimberley A.M., King A., Laird G.K., Langford C.F.,
RA Leversha M.A., Lloyd C., Lloyd D.M., Martyn I.D., Mashreghi-Mohammadi M.,
RA Matthews L.H., Mccann O.T., Mcclay J., Mclaren S., McMurray A.A.,
RA Milne S.A., Mortimore B.J., Odell C.N., Pavitt R., Pearce A.V., Pearson D.,
RA Phillimore B.J.C.T., Phillips S.H., Plumb R.W., Ramsay H., Ramsey Y.,
RA Rogers L., Ross M.T., Scott C.E., Sehra H.K., Skuce C.D., Smalley S.,
RA Smith M.L., Soderlund C., Spragon L., Steward C.A., Sulston J.E.,
RA Swann R.M., Vaudin M., Wall M., Wallis J.M., Whiteley M.N., Willey D.L.,
RA Williams L., Williams S.A., Williamson H., Wilmer T.E., Wilming L.,
RA Wright C.L., Hubbard T., Bentley D.R., Beck S., Rogers J., Shimizu N.,
RA Minoshima S., Kawasaki K., Sasaki T., Asakawa S., Kudoh J., Shintani A.,
RA Shibuya K., Yoshizaki Y., Aoki N., Mitsuyama S., Roe B.A., Chen F., Chu L.,
RA Crabtree J., Deschamps S., Do A., Do T., Dorman A., Fang F., Fu Y., Hu P.,
RA Hua A., Kenton S., Lai H., Lao H.I., Lewis J., Lewis S., Lin S.-P., Loh P.,
RA Malaj E., Nguyen T., Pan H., Phan S., Qi S., Qian Y., Ray L., Ren Q.,
RA Shaull S., Sloan D., Song L., Wang Q., Wang Y., Wang Z., White J.,
RA Willingham D., Wu H., Yao Z., Zhan M., Zhang G., Chissoe S., Murray J.,
RA Miller N., Minx P., Fulton R., Johnson D., Bemis G., Bentley D.,
RA Bradshaw H., Bourne S., Cordes M., Du Z., Fulton L., Goela D., Graves T.,
RA Hawkins J., Hinds K., Kemp K., Latreille P., Layman D., Ozersky P.,
RA Rohlfing T., Scheet P., Walker C., Wamsley A., Wohldmann P., Pepin K.,
RA Nelson J., Korf I., Bedell J.A., Hillier L.W., Mardis E., Waterston R.,
RA Wilson R., Emanuel B.S., Shaikh T., Kurahashi H., Saitta S., Budarf M.L.,
RA McDermid H.E., Johnson A., Wong A.C.C., Morrow B.E., Edelmann L., Kim U.J.,
RA Shizuya H., Simon M.I., Dumanski J.P., Peyrard M., Kedra D., Seroussi E.,
RA Fransson I., Tapia I., Bruder C.E., O'Brien K.P., Wilkinson P.,
RA Bodenteich A., Hartman K., Hu X., Khan A.S., Lane L., Tilahun Y.,
RA Wright H.;
RT "The DNA sequence of human chromosome 22.";
RL Nature 402:489-495(1999).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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 [8]
RP INTERACTION WITH SMN1.
RX PubMed=10500148; DOI=10.1073/pnas.96.20.11167;
RA Pellizzoni L., Charroux B., Dreyfuss G.;
RT "SMN mutants of spinal muscular atrophy patients are defective in binding
RT to snRNP proteins.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:11167-11172(1999).
RN [9]
RP METHYLATION.
RX PubMed=11747828; DOI=10.1016/s0960-9822(01)00592-9;
RA Meister G., Eggert C., Buehler D., Brahms H., Kambach C., Fischer U.;
RT "Methylation of Sm proteins by a complex containing PRMT5 and the putative
RT U snRNP assembly factor pICln.";
RL Curr. Biol. 11:1990-1994(2001).
RN [10]
RP INTERACTION WITH SMN1.
RX PubMed=11135666; DOI=10.1038/83014;
RA Selenko P., Sprangers R., Stier G., Buhler D., Fischer U., Sattler M.;
RT "SMN tudor domain structure and its interaction with the Sm proteins.";
RL Nat. Struct. Biol. 8:27-31(2001).
RN [11]
RP IDENTIFICATION IN THE U7 SNRNP COMPLEX, SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=11574479; DOI=10.1093/emboj/20.19.5470;
RA Pillai R.S., Will C.L., Luehrmann R., Schuemperli D., Mueller B.;
RT "Purified U7 snRNPs lack the Sm proteins D1 and D2 but contain Lsm10, a new
RT 14 kDa Sm D1-like protein.";
RL EMBO J. 20:5470-5479(2001).
RN [12]
RP IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE SPLICEOSOMAL C
RP COMPLEX, FUNCTION, SUBCELLULAR LOCATION, AND SUBUNIT.
RX PubMed=11991638; DOI=10.1017/s1355838202021088;
RA Jurica M.S., Licklider L.J., Gygi S.P., Grigorieff N., Moore M.J.;
RT "Purification and characterization of native spliceosomes suitable for
RT three-dimensional structural analysis.";
RL RNA 8:426-439(2002).
RN [13]
RP INTERACTION WITH SMN1.
RX PubMed=12628254; DOI=10.1016/s0022-2836(03)00148-7;
RA Sprangers R., Groves M.R., Sinning I., Sattler M.;
RT "High-resolution X-ray and NMR structures of the SMN Tudor domain:
RT conformational variation in the binding site for symmetrically dimethylated
RT arginine residues.";
RL J. Mol. Biol. 327:507-520(2003).
RN [14]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC TISSUE=Lymphoblast;
RX PubMed=14654843; DOI=10.1038/nature02166;
RA Andersen J.S., Wilkinson C.J., Mayor T., Mortensen P., Nigg E.A., Mann M.;
RT "Proteomic characterization of the human centrosome by protein correlation
RT profiling.";
RL Nature 426:570-574(2003).
RN [15]
RP IDENTIFICATION IN A COMPLEX WITH THE U11/U12 SPLICEOSOME, IDENTIFICATION BY
RP MASS SPECTROMETRY, AND SUBUNIT.
RX PubMed=15146077; DOI=10.1261/rna.7320604;
RA Will C.L., Schneider C., Hossbach M., Urlaub H., Rauhut R., Elbashir S.,
RA Tuschl T., Luehrmann R.;
RT "The human 18S U11/U12 snRNP contains a set of novel proteins not found in
RT the U2-dependent spliceosome.";
RL RNA 10:929-941(2004).
RN [16]
RP IDENTIFICATION IN THE SMN-SM COMPLEX.
RX PubMed=16314521; DOI=10.1128/mcb.25.24.10989-11004.2005;
RA Golembe T.J., Yong J., Dreyfuss G.;
RT "Specific sequence features, recognized by the SMN complex, identify snRNAs
RT and determine their fate as snRNPs.";
RL Mol. Cell. Biol. 25:10989-11004(2005).
RN [17]
RP METHYLATION, AND INTERACTION WITH PRMT5 AND PRMT7.
RX PubMed=17709427; DOI=10.1083/jcb.200702147;
RA Gonsalvez G.B., Tian L., Ospina J.K., Boisvert F.-M., Lamond A.I.,
RA Matera A.G.;
RT "Two distinct arginine methyltransferases are required for biogenesis of
RT Sm-class ribonucleoproteins.";
RL J. Cell Biol. 178:733-740(2007).
RN [18]
RP FUNCTION IN SNRNP BIOGENESIS, IDENTIFICATION IN 6S PICLN-SM COMPLEX,
RP IDENTIFICATION IN SMN-SM COMPLEX, AND SUBCELLULAR LOCATION.
RX PubMed=18984161; DOI=10.1016/j.cell.2008.09.020;
RA Chari A., Golas M.M., Klingenhager M., Neuenkirchen N., Sander B.,
RA Englbrecht C., Sickmann A., Stark H., Fischer U.;
RT "An assembly chaperone collaborates with the SMN complex to generate
RT spliceosomal SnRNPs.";
RL Cell 135:497-509(2008).
RN [19]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=19413330; DOI=10.1021/ac9004309;
RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.;
RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in a
RT refined SCX-based approach.";
RL Anal. Chem. 81:4493-4501(2009).
RN [20]
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 [21]
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 [22]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 4-75 IN COMPLEX WITH SNRPB.
RX PubMed=10025403; DOI=10.1016/s0092-8674(00)80550-4;
RA Kambach C., Walke S., Young R., Avis J.M., de la Fortelle E., Raker V.A.,
RA Luehrmann R., Li J., Nagai K.;
RT "Crystal structures of two Sm protein complexes and their implications for
RT the assembly of the spliceosomal snRNPs.";
RL Cell 96:375-387(1999).
RN [23]
RP X-RAY CRYSTALLOGRAPHY (5.49 ANGSTROMS) IN SPLICEOSOMAL U1 SNRNP, FUNCTION,
RP AND SUBUNIT.
RX PubMed=19325628; DOI=10.1038/nature07851;
RA Pomeranz Krummel D.A., Oubridge C., Leung A.K., Li J., Nagai K.;
RT "Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution.";
RL Nature 458:475-480(2009).
RN [24]
RP X-RAY CRYSTALLOGRAPHY (3.60 ANGSTROMS) IN SPLICEOSOMAL CORE U4 SNRNP, AND
RP SUBUNIT.
RX PubMed=21516107; DOI=10.1038/nature09956;
RA Leung A.K., Nagai K., Li J.;
RT "Structure of the spliceosomal U4 snRNP core domain and its implication for
RT snRNP biogenesis.";
RL Nature 473:536-539(2011).
RN [25] {ECO:0007744|PDB:4PJO}
RP X-RAY CRYSTALLOGRAPHY (3.30 ANGSTROMS), AND SUBUNIT.
RX PubMed=25555158; DOI=10.7554/elife.04986;
RA Kondo Y., Oubridge C., van Roon A.M., Nagai K.;
RT "Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein
RT particle, reveals the mechanism of 5' splice site recognition.";
RL Elife 4:0-0(2015).
RN [26] {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 [27] {ECO:0007744|PDB:5XJC}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.60 ANGSTROMS), FUNCTION, SUBCELLULAR
RP LOCATION, AND SUBUNIT.
RX PubMed=28502770; DOI=10.1016/j.cell.2017.04.033;
RA Zhang X., Yan C., Hang J., Finci L.I., Lei J., Shi Y.;
RT "An Atomic Structure of the Human Spliceosome.";
RL Cell 169:918-929(2017).
RN [28] {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).
RN [29] {ECO:0007744|PDB:5MQF}
RP STRUCTURE BY ELECTRON MICROSCOPY (5.90 ANGSTROMS), FUNCTION, SUBCELLULAR
RP LOCATION, SUBUNIT, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=28076346; DOI=10.1038/nature21079;
RA Bertram K., Agafonov D.E., Liu W.T., Dybkov O., Will C.L., Hartmuth K.,
RA Urlaub H., Kastner B., Stark H., Luhrmann R.;
RT "Cryo-EM structure of a human spliceosome activated for step 2 of
RT splicing.";
RL Nature 542:318-323(2017).
CC -!- FUNCTION: Plays a role in pre-mRNA splicing as a core component of the
CC spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins
CC (snRNPs), the building blocks of the spliceosome (PubMed:11991638,
CC PubMed:18984161, PubMed:19325628, PubMed:25555158, PubMed:26912367,
CC PubMed:28502770, PubMed:28781166, PubMed:28076346). Component of both
CC the pre-catalytic spliceosome B complex and activated spliceosome C
CC complexes (PubMed:11991638, PubMed:28502770, PubMed:28781166,
CC PubMed:28076346). Is also a component of the minor U12 spliceosome
CC (PubMed:15146077). As part of the U7 snRNP it is involved in histone
CC pre-mRNA 3'-end processing (By similarity).
CC {ECO:0000250|UniProtKB:P62320, ECO:0000269|PubMed:11991638,
CC ECO:0000269|PubMed:15146077, ECO:0000269|PubMed:18984161,
CC ECO:0000269|PubMed:19325628, ECO:0000269|PubMed:25555158,
CC ECO:0000269|PubMed:26912367, ECO:0000269|PubMed:28076346,
CC ECO:0000269|PubMed:28502770, ECO:0000269|PubMed:28781166}.
CC -!- SUBUNIT: Core component of the spliceosomal U1, U2, U4 and U5 small
CC nuclear ribonucleoproteins (snRNPs), the building blocks of the
CC spliceosome (PubMed:11991638, PubMed:10025403, PubMed:19325628,
CC PubMed:21516107, PubMed:25555158, PubMed:26912367, PubMed:28502770,
CC PubMed:28781166, PubMed:28076346). Most spliceosomal snRNPs contain a
CC common set of Sm proteins, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF
CC and SNRPG that assemble in a heptameric protein ring on the Sm site of
CC the small nuclear RNA to form the core snRNP (PubMed:10025403,
CC PubMed:19325628, PubMed:21516107, PubMed:25555158, PubMed:26912367,
CC PubMed:28502770, PubMed:28781166, PubMed:28076346). Component of the U1
CC snRNP (PubMed:19325628, PubMed:25555158). The U1 snRNP is composed of
CC the U1 snRNA and the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3,
CC SNRPE, SNRPF and SNRPG, and at least three U1 snRNP-specific proteins
CC SNRNP70/U1-70K, SNRPA/U1-A and SNRPC/U1-C (PubMed:19325628,
CC PubMed:25555158). Component of the U4/U6-U5 tri-snRNP complex composed
CC of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8,
CC PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3,
CC SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and
CC USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8
CC (PubMed:26912367). Component of the U7 snRNP complex, or U7 Sm protein
CC core complex, that is composed of the U7 snRNA and at least LSM10,
CC LSM11, SNRPB, SNRPD3, SNRPE, SNRPF and SNRPG; the complex does not
CC contain SNRPD1 and SNRPD2 (PubMed:11574479). Component of the U11/U12
CC snRNPs that are part of the U12-type spliceosome (PubMed:15146077).
CC Part of the SMN-Sm complex that contains SMN1, GEMIN2/SIP1,
CC DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8, STRAP/UNRIP and
CC the Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG;
CC catalyzes core snRNPs assembly (PubMed:16314521). Forms a 6S pICln-Sm
CC complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and
CC SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm
CC proteins and which is unable to assemble into the core snRNP. Interacts
CC (via C-terminus) with SMN1 (via Tudor domain); the interaction is
CC direct (PubMed:12628254, PubMed:10500148, PubMed:11135666).
CC {ECO:0000269|PubMed:10025403, ECO:0000269|PubMed:10500148,
CC ECO:0000269|PubMed:11135666, ECO:0000269|PubMed:11574479,
CC ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:12628254,
CC ECO:0000269|PubMed:15146077, ECO:0000269|PubMed:16314521,
CC ECO:0000269|PubMed:18984161, ECO:0000269|PubMed:19325628,
CC ECO:0000269|PubMed:21516107, ECO:0000269|PubMed:25555158,
CC ECO:0000269|PubMed:26912367, ECO:0000269|PubMed:28076346,
CC ECO:0000269|PubMed:28502770, ECO:0000269|PubMed:28781166}.
CC -!- INTERACTION:
CC P62318; P54253: ATXN1; NbExp=3; IntAct=EBI-372789, EBI-930964;
CC P62318; P54105: CLNS1A; NbExp=9; IntAct=EBI-372789, EBI-724693;
CC P62318; P84090: ERH; NbExp=3; IntAct=EBI-372789, EBI-711389;
CC P62318; P62310: LSM3; NbExp=5; IntAct=EBI-372789, EBI-348239;
CC P62318; Q9UK45: LSM7; NbExp=3; IntAct=EBI-372789, EBI-348372;
CC P62318; Q96HA8: NTAQ1; NbExp=3; IntAct=EBI-372789, EBI-741158;
CC P62318; P14678: SNRPB; NbExp=4; IntAct=EBI-372789, EBI-372458;
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol {ECO:0000269|PubMed:18984161}.
CC Nucleus {ECO:0000269|PubMed:11574479, ECO:0000269|PubMed:11991638,
CC ECO:0000269|PubMed:26912367, ECO:0000269|PubMed:28076346,
CC ECO:0000269|PubMed:28502770, ECO:0000269|PubMed:28781166}. Note=SMN-
CC mediated assembly into core snRNPs occurs in the cytosol before SMN-
CC mediated transport to the nucleus to be included in spliceosomes.
CC {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=P62318-1; Sequence=Displayed;
CC Name=2;
CC IsoId=P62318-2; Sequence=VSP_056478;
CC -!- PTM: Methylated on arginine residues by PRMT5 and PRMT7; probable
CC asymmetric dimethylation which is required for assembly and biogenesis
CC of snRNPs. {ECO:0000269|PubMed:11747828, ECO:0000269|PubMed:17709427}.
CC -!- MISCELLANEOUS: In the autoimmune disease systemic lupus erythematosus,
CC antinuclear antibodies are developed with Sm specificity.
CC -!- SIMILARITY: Belongs to the snRNP core protein family. {ECO:0000305}.
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DR EMBL; U15009; AAA57034.1; -; mRNA.
DR EMBL; CR456583; CAG30469.1; -; mRNA.
DR EMBL; AK296173; BAG58909.1; -; mRNA.
DR EMBL; AB451249; BAG70063.1; -; mRNA.
DR EMBL; AB451373; BAG70187.1; -; mRNA.
DR EMBL; AP000356; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471095; EAW59670.1; -; Genomic_DNA.
DR EMBL; BC000457; AAH00457.1; -; mRNA.
DR EMBL; BC003150; AAH03150.1; -; mRNA.
DR CCDS; CCDS13828.1; -. [P62318-1]
DR RefSeq; NP_001265585.1; NM_001278656.1. [P62318-1]
DR RefSeq; NP_004166.1; NM_004175.4. [P62318-1]
DR PDB; 1D3B; X-ray; 2.00 A; A/C/E/G/I/K=1-75.
DR PDB; 3CW1; X-ray; 5.49 A; D/S/T/U=1-126.
DR PDB; 3JCR; EM; 7.00 A; R/r=1-126.
DR PDB; 3PGW; X-ray; 4.40 A; W/Z=1-126.
DR PDB; 3VRI; X-ray; 1.60 A; C=54-63.
DR PDB; 4PJO; X-ray; 3.30 A; A/O/a/o=1-126.
DR PDB; 4WZJ; X-ray; 3.60 A; AD/AK/AR/BD/BK/BR/CD/CK/CR/DD/DK/DR=1-126.
DR PDB; 5MQF; EM; 5.90 A; e/l=1-126.
DR PDB; 5O9Z; EM; 4.50 A; W/e/l=1-126.
DR PDB; 5XJC; EM; 3.60 A; a/h=1-126.
DR PDB; 5YZG; EM; 4.10 A; a/h=1-126.
DR PDB; 5Z56; EM; 5.10 A; a/h=1-126.
DR PDB; 5Z57; EM; 6.50 A; a/h=1-126.
DR PDB; 5Z58; EM; 4.90 A; a/h=1-126.
DR PDB; 6AH0; EM; 5.70 A; T/e/h=1-126.
DR PDB; 6AHD; EM; 3.80 A; T/g/h=1-126.
DR PDB; 6FF7; EM; 4.50 A; e/l=1-126.
DR PDB; 6ICZ; EM; 3.00 A; a/h=1-126.
DR PDB; 6ID0; EM; 2.90 A; a/h=1-126.
DR PDB; 6ID1; EM; 2.86 A; a/h=1-126.
DR PDB; 6QDV; EM; 3.30 A; d/n=2-85.
DR PDB; 6QW6; EM; 2.92 A; 43/53=1-126.
DR PDB; 6QX9; EM; 3.28 A; 13/23/43/53=1-126.
DR PDB; 6V4X; EM; 3.20 A; A=1-126.
DR PDB; 6Y53; EM; 7.10 A; l=1-126.
DR PDB; 6Y5Q; EM; 7.10 A; l=1-126.
DR PDB; 7A5P; EM; 5.00 A; a/l=1-126.
DR PDB; 7ABG; EM; 7.80 A; e/l=1-126.
DR PDB; 7ABI; EM; 8.00 A; e/l=1-126.
DR PDB; 7B0Y; EM; 3.60 A; i=1-126.
DR PDB; 7DVQ; EM; 2.89 A; a/h=1-126.
DR PDBsum; 1D3B; -.
DR PDBsum; 3CW1; -.
DR PDBsum; 3JCR; -.
DR PDBsum; 3PGW; -.
DR PDBsum; 3VRI; -.
DR PDBsum; 4PJO; -.
DR PDBsum; 4WZJ; -.
DR PDBsum; 5MQF; -.
DR PDBsum; 5O9Z; -.
DR PDBsum; 5XJC; -.
DR PDBsum; 5YZG; -.
DR PDBsum; 5Z56; -.
DR PDBsum; 5Z57; -.
DR PDBsum; 5Z58; -.
DR PDBsum; 6AH0; -.
DR PDBsum; 6AHD; -.
DR PDBsum; 6FF7; -.
DR PDBsum; 6ICZ; -.
DR PDBsum; 6ID0; -.
DR PDBsum; 6ID1; -.
DR PDBsum; 6QDV; -.
DR PDBsum; 6QW6; -.
DR PDBsum; 6QX9; -.
DR PDBsum; 6V4X; -.
DR PDBsum; 6Y53; -.
DR PDBsum; 6Y5Q; -.
DR PDBsum; 7A5P; -.
DR PDBsum; 7ABG; -.
DR PDBsum; 7ABI; -.
DR PDBsum; 7B0Y; -.
DR PDBsum; 7DVQ; -.
DR AlphaFoldDB; P62318; -.
DR SMR; P62318; -.
DR BioGRID; 112518; 336.
DR ComplexPortal; CPX-2391; U4/U6.U5 small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-2392; U1 small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-2539; U2 small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-6033; Sm complex.
DR CORUM; P62318; -.
DR DIP; DIP-31216N; -.
DR IntAct; P62318; 92.
DR MINT; P62318; -.
DR STRING; 9606.ENSP00000215829; -.
DR CarbonylDB; P62318; -.
DR GlyGen; P62318; 1 site, 1 O-linked glycan (1 site).
DR iPTMnet; P62318; -.
DR MetOSite; P62318; -.
DR PhosphoSitePlus; P62318; -.
DR SwissPalm; P62318; -.
DR BioMuta; SNRPD3; -.
DR DMDM; 51338667; -.
DR EPD; P62318; -.
DR jPOST; P62318; -.
DR MassIVE; P62318; -.
DR MaxQB; P62318; -.
DR PaxDb; P62318; -.
DR PeptideAtlas; P62318; -.
DR PRIDE; P62318; -.
DR ProteomicsDB; 4397; -.
DR ProteomicsDB; 57393; -. [P62318-1]
DR TopDownProteomics; P62318-1; -. [P62318-1]
DR ABCD; P62318; 7 sequenced antibodies.
DR Antibodypedia; 216; 221 antibodies from 32 providers.
DR DNASU; 6634; -.
DR Ensembl; ENST00000215829.8; ENSP00000215829.3; ENSG00000100028.12. [P62318-1]
DR Ensembl; ENST00000402849.5; ENSP00000385266.1; ENSG00000100028.12. [P62318-2]
DR GeneID; 6634; -.
DR KEGG; hsa:6634; -.
DR MANE-Select; ENST00000215829.8; ENSP00000215829.3; NM_004175.5; NP_004166.1.
DR UCSC; uc003aam.3; human. [P62318-1]
DR CTD; 6634; -.
DR DisGeNET; 6634; -.
DR GeneCards; SNRPD3; -.
DR HGNC; HGNC:11160; SNRPD3.
DR HPA; ENSG00000100028; Low tissue specificity.
DR MIM; 601062; gene.
DR neXtProt; NX_P62318; -.
DR OpenTargets; ENSG00000100028; -.
DR PharmGKB; PA36001; -.
DR VEuPathDB; HostDB:ENSG00000100028; -.
DR eggNOG; KOG3172; Eukaryota.
DR GeneTree; ENSGT00610000086153; -.
DR HOGENOM; CLU_099537_1_0_1; -.
DR InParanoid; P62318; -.
DR OMA; MNCQLRD; -.
DR OrthoDB; 1584810at2759; -.
DR PhylomeDB; P62318; -.
DR TreeFam; TF354302; -.
DR PathwayCommons; P62318; -.
DR Reactome; R-HSA-111367; SLBP independent Processing of Histone Pre-mRNAs.
DR Reactome; R-HSA-191859; snRNP Assembly.
DR Reactome; R-HSA-72163; mRNA Splicing - Major Pathway.
DR Reactome; R-HSA-72165; mRNA Splicing - Minor Pathway.
DR Reactome; R-HSA-73856; RNA Polymerase II Transcription Termination.
DR Reactome; R-HSA-77588; SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs.
DR Reactome; R-HSA-9754678; SARS-CoV-2 modulates host translation machinery.
DR SignaLink; P62318; -.
DR BioGRID-ORCS; 6634; 801 hits in 1057 CRISPR screens.
DR ChiTaRS; SNRPD3; human.
DR EvolutionaryTrace; P62318; -.
DR GeneWiki; SNRPD3; -.
DR GenomeRNAi; 6634; -.
DR Pharos; P62318; Tbio.
DR PRO; PR:P62318; -.
DR Proteomes; UP000005640; Chromosome 22.
DR RNAct; P62318; protein.
DR Bgee; ENSG00000100028; Expressed in ganglionic eminence and 112 other tissues.
DR Genevisible; P62318; HS.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; IDA:UniProtKB.
DR GO; GO:0000243; C:commitment complex; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IDA:UniProtKB.
DR GO; GO:0034709; C:methylosome; IDA:UniProtKB.
DR GO; GO:0016604; C:nuclear body; IDA:HPA.
DR GO; GO:0005654; C:nucleoplasm; IDA:HPA.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0034715; C:pICln-Sm protein complex; IDA:UniProtKB.
DR GO; GO:0071011; C:precatalytic spliceosome; IBA:GO_Central.
DR GO; GO:0030532; C:small nuclear ribonucleoprotein complex; TAS:ProtInc.
DR GO; GO:0034719; C:SMN-Sm protein complex; IDA:UniProtKB.
DR GO; GO:0005681; C:spliceosomal complex; IPI:ComplexPortal.
DR GO; GO:0097526; C:spliceosomal tri-snRNP complex; IBA:GO_Central.
DR GO; GO:0005697; C:telomerase holoenzyme complex; IDA:BHF-UCL.
DR GO; GO:0005685; C:U1 snRNP; IDA:UniProtKB.
DR GO; GO:0005689; C:U12-type spliceosomal complex; IDA:UniProtKB.
DR GO; GO:0005686; C:U2 snRNP; IBA:GO_Central.
DR GO; GO:0071007; C:U2-type catalytic step 2 spliceosome; IDA:UniProtKB.
DR GO; GO:0071005; C:U2-type precatalytic spliceosome; IDA:UniProtKB.
DR GO; GO:0005687; C:U4 snRNP; IDA:UniProtKB.
DR GO; GO:0046540; C:U4/U6 x U5 tri-snRNP complex; IDA:UniProtKB.
DR GO; GO:0005682; C:U5 snRNP; IBA:GO_Central.
DR GO; GO:0005683; C:U7 snRNP; IDA:UniProtKB.
DR GO; GO:0019899; F:enzyme binding; IPI:UniProtKB.
DR GO; GO:0071208; F:histone pre-mRNA DCP binding; ISS:UniProtKB.
DR GO; GO:0003723; F:RNA binding; IPI:BHF-UCL.
DR GO; GO:0070034; F:telomerase RNA binding; IPI:BHF-UCL.
DR GO; GO:0071209; F:U7 snRNA binding; IPI:BHF-UCL.
DR GO; GO:0036261; P:7-methylguanosine cap hypermethylation; IC:ComplexPortal.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IDA:UniProtKB.
DR GO; GO:0006479; P:protein methylation; IDA:MGI.
DR GO; GO:0008380; P:RNA splicing; TAS:ProtInc.
DR GO; GO:0000387; P:spliceosomal snRNP assembly; IDA:UniProtKB.
DR GO; GO:1903241; P:U2-type prespliceosome assembly; IC:ComplexPortal.
DR CDD; cd01721; Sm_D3; 1.
DR DisProt; DP01704; -.
DR IDEAL; IID00161; -.
DR InterPro; IPR027141; LSm4/Sm_D1/D3.
DR InterPro; IPR001163; LSM_dom_euk/arc.
DR InterPro; IPR010920; LSM_dom_sf.
DR InterPro; IPR034099; SmD3.
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; Alternative splicing; Cytoplasm;
KW Direct protein sequencing; Methylation; mRNA processing; mRNA splicing;
KW Nucleus; Reference proteome; Repeat; Ribonucleoprotein; RNA-binding;
KW Spliceosome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:19413330"
FT CHAIN 2..126
FT /note="Small nuclear ribonucleoprotein Sm D3"
FT /id="PRO_0000122214"
FT REPEAT 110..111
FT /note="1"
FT REPEAT 112..113
FT /note="2"
FT REPEAT 114..115
FT /note="3"
FT REPEAT 116..117
FT /note="4"
FT REPEAT 118..119
FT /note="5"
FT REGION 110..119
FT /note="5 X 2 AA tandem repeats of [RM]-G; required for
FT interaction with SMN1"
FT /evidence="ECO:0000269|PubMed:12628254"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:19413330"
FT VAR_SEQ 107..126
FT /note="VAARGRGRGMGRGNIFQKRR -> GYLSSLEWVLVHIC (in isoform
FT 2)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_056478"
FT HELIX 6..12
FT /evidence="ECO:0007829|PDB:1D3B"
FT TURN 13..15
FT /evidence="ECO:0007829|PDB:1D3B"
FT STRAND 16..22
FT /evidence="ECO:0007829|PDB:1D3B"
FT STRAND 27..35
FT /evidence="ECO:0007829|PDB:1D3B"
FT STRAND 37..39
FT /evidence="ECO:0007829|PDB:4PJO"
FT STRAND 41..49
FT /evidence="ECO:0007829|PDB:1D3B"
FT STRAND 55..63
FT /evidence="ECO:0007829|PDB:1D3B"
FT HELIX 65..67
FT /evidence="ECO:0007829|PDB:1D3B"
FT STRAND 68..73
FT /evidence="ECO:0007829|PDB:1D3B"
FT STRAND 75..77
FT /evidence="ECO:0007829|PDB:6ID1"
SQ SEQUENCE 126 AA; 13916 MW; 59A6E78E860AA3E0 CRC64;
MSIGVPIKVL HEAEGHIVTC ETNTGEVYRG KLIEAEDNMN CQMSNITVTY RDGRVAQLEQ
VYIRGSKIRF LILPDMLKNA PMLKSMKNKN QGSGAGRGKA AILKAQVAAR GRGRGMGRGN
IFQKRR
