SMD2_HUMAN
ID SMD2_HUMAN Reviewed; 118 AA.
AC P62316; A8K797; J3KPM5; P43330;
DT 05-JUL-2004, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 186.
DE RecName: Full=Small nuclear ribonucleoprotein Sm D2;
DE Short=Sm-D2;
DE AltName: Full=snRNP core protein D2;
GN Name=SNRPD2; Synonyms=SNRPD1;
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 PROTEIN SEQUENCE OF 75-96 AND
RP 103-118.
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=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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15057824; DOI=10.1038/nature02399;
RA Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E.,
RA Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A.,
RA Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S.,
RA Carrano A.V., Caoile C., Chan Y.M., Christensen M., Cleland C.A.,
RA Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J.,
RA Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M.,
RA Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W.,
RA Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V.,
RA Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D.,
RA McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I.,
RA Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L.,
RA Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A.,
RA She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M.,
RA Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J.,
RA Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E.,
RA Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M.,
RA Rubin E.M., Lucas S.M.;
RT "The DNA sequence and biology of human chromosome 19.";
RL Nature 428:529-535(2004).
RN [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
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 2-47; 72-79 AND 103-118, CLEAVAGE OF INITIATOR
RP METHIONINE, ACETYLATION AT SER-2, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC TISSUE=Cervix carcinoma, and Mammary carcinoma;
RA Bienvenut W.V., Calvo F., Matallanas D., Cooper W.N., Kolch W.;
RL Submitted (FEB-2008) to UniProtKB.
RN [7]
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 [8]
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 [9]
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 [10]
RP IDENTIFICATION IN A COMPLEX WITH THE U11/U12 SPLICEOSOME, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
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 [11]
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 [12]
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 [13]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-12, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full phosphorylation
RT site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [15]
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 [16]
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=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [17]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-9 AND THR-12, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma, and Erythroleukemia;
RX PubMed=23186163; DOI=10.1021/pr300630k;
RA Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
RA Mohammed S.;
RT "Toward a comprehensive characterization of a human cancer cell
RT phosphoproteome.";
RL J. Proteome Res. 12:260-271(2013).
RN [18]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=25772364; DOI=10.1016/j.celrep.2015.02.033;
RA Hendriks I.A., Treffers L.W., Verlaan-de Vries M., Olsen J.V.,
RA Vertegaal A.C.;
RT "SUMO-2 orchestrates chromatin modifiers in response to DNA damage.";
RL Cell Rep. 10:1778-1791(2015).
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=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 [20]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-6 AND LYS-8, AND IDENTIFICATION
RP BY MASS 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 [21]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 26-118 IN COMPLEX WITH SNRPD1, AND
RP SUBUNIT.
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 [22]
RP X-RAY CRYSTALLOGRAPHY (5.49 ANGSTROMS) IN SPLICEOSOMAL U1 SNRNP, SUBUNIT,
RP AND FUNCTION.
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 [23] {ECO:0007744|PDB:5XJL}
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) IN COMPLEX WITH SNRPD1; SNRPE;
RP SNRPF; SNRPG; SMN1 AND GEMIN2, AND INTERACTION WITH SNRPD1; GEMIN2 AND
RP SNRPF.
RX PubMed=21816274; DOI=10.1016/j.cell.2011.06.043;
RA Zhang R., So B.R., Li P., Yong J., Glisovic T., Wan L., Dreyfuss G.;
RT "Structure of a key intermediate of the SMN complex reveals Gemin2's
RT crucial function in snRNP assembly.";
RL Cell 146:384-395(2011).
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]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN 6S PICLN-SM COMPLEX,
RP IDENTIFICATION IN 6S PICLN-SM COMPLEX, AND FUNCTION IN CORE U1 SNRNP
RP BIOGENESIS.
RX PubMed=23333303; DOI=10.1016/j.molcel.2012.12.009;
RA Grimm C., Chari A., Pelz J.P., Kuper J., Kisker C., Diederichs K.,
RA Stark H., Schindelin H., Fischer U.;
RT "Structural basis of assembly chaperone-mediated snRNP formation.";
RL Mol. Cell 49:692-703(2013).
RN [26] {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 [27] {ECO:0007744|PDB:3JCR}
RP STRUCTURE BY ELECTRON MICROSCOPY (7.00 ANGSTROMS), FUNCTION, SUBCELLULAR
RP LOCATION, 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 [28] {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 [29] {ECO:0007744|PDB:5O9Z}
RP STRUCTURE BY ELECTRON MICROSCOPY (4.50 ANGSTROMS), IDENTIFICATION BY MASS
RP SPECTROMETRY, FUNCTION, SUBCELLULAR LOCATION, AND SUBUNIT.
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 [30] {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).
RN [31] {ECO:0007744|PDB:5XJQ, ECO:0007744|PDB:5XJR, ECO:0007744|PDB:5XJS}
RP X-RAY CRYSTALLOGRAPHY (3.12 ANGSTROMS) IN COMPLEX WITH GEMIN2; SNRPD1;
RP SNRPE; SNRPF; SNRPG AND SMN1, AND INTERACTION WITH GEMIN2; SNRPD1 AND
RP SNRPF.
RX PubMed=31799625; DOI=10.1093/nar/gkz1135;
RA Yi H., Mu L., Shen C., Kong X., Wang Y., Hou Y., Zhang R.;
RT "Negative cooperativity between Gemin2 and RNA provides insights into RNA
RT selection and the SMN complex's release in snRNP assembly.";
RL Nucleic Acids Res. 48:895-911(2020).
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:23333303, PubMed:25555158,
CC PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346).
CC Component of both the pre-catalytic spliceosome B complex and activated
CC spliceosome C complexes (PubMed:11991638, PubMed:28502770,
CC PubMed:28781166, PubMed:28076346). Is also a component of the minor U12
CC spliceosome (PubMed:15146077). {ECO:0000269|PubMed:11991638,
CC ECO:0000269|PubMed:15146077, ECO:0000269|PubMed:18984161,
CC ECO:0000269|PubMed:19325628, ECO:0000269|PubMed:23333303,
CC ECO:0000269|PubMed:25555158, ECO:0000269|PubMed:26912367,
CC ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770,
CC 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:19325628, PubMed:21516107,
CC PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166,
CC PubMed:28076346). Most spliceosomal snRNPs contain a common set of Sm
CC proteins, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that
CC assemble in a heptameric protein ring on the Sm site of the small
CC nuclear RNA to form the core snRNP (PubMed:10025403, PubMed:19325628,
CC PubMed:21516107, PubMed:25555158, PubMed:26912367, PubMed:28502770,
CC PubMed:28781166, PubMed:28076346). Component of the U1 snRNP
CC (PubMed:19325628, PubMed:25555158). The U1 snRNP is composed of the U1
CC snRNA and the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE,
CC 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 U11/U12 snRNPs that are part of the
CC U12-type spliceosome (PubMed:15146077). Part of the SMN-Sm complex that
CC contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6,
CC GEMIN7, GEMIN8, STRAP/UNRIP and the Sm proteins SNRPB, SNRPD1, SNRPD2,
CC SNRPD3, SNRPE, SNRPF and SNRPG; catalyzes core snRNPs assembly
CC (PubMed:16314521). Forms a 6S pICln-Sm complex composed of
CC CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like
CC structure where CLNS1A/pICln mimics additional Sm proteins and which is
CC unable to assemble into the core snRNP. Interacts with SMN1; the
CC interaction is direct (PubMed:21816274). Interacts with GEMIN2; the
CC interaction is direct (PubMed:21816274, PubMed:31799625). Interacts
CC with SNRPD1; the interaction is direct (PubMed:21816274,
CC PubMed:31799625). Interacts with SNRPF; the interaction is direct
CC (PubMed:21816274, PubMed:31799625). {ECO:0000269|PubMed:10025403,
CC ECO:0000269|PubMed:10500148, ECO:0000269|PubMed:11991638,
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:21816274,
CC ECO:0000269|PubMed:23333303, ECO:0000269|PubMed:25555158,
CC ECO:0000269|PubMed:26912367, ECO:0000269|PubMed:28076346,
CC ECO:0000269|PubMed:28502770, ECO:0000269|PubMed:28781166,
CC ECO:0000269|PubMed:31799625}.
CC -!- INTERACTION:
CC P62316; P54253: ATXN1; NbExp=3; IntAct=EBI-297993, EBI-930964;
CC P62316; Q8NHQ1: CEP70; NbExp=3; IntAct=EBI-297993, EBI-739624;
CC P62316; Q9BW66: CINP; NbExp=3; IntAct=EBI-297993, EBI-739784;
CC P62316; P54105: CLNS1A; NbExp=11; IntAct=EBI-297993, EBI-724693;
CC P62316; P42858: HTT; NbExp=3; IntAct=EBI-297993, EBI-466029;
CC P62316; Q9Y333: LSM2; NbExp=3; IntAct=EBI-297993, EBI-347416;
CC P62316; P62312: LSM6; NbExp=3; IntAct=EBI-297993, EBI-373310;
CC P62316; P62314: SNRPD1; NbExp=3; IntAct=EBI-297993, EBI-372177;
CC P62316; P62306: SNRPF; NbExp=11; IntAct=EBI-297993, EBI-356900;
CC P62316; Q5MJ10: SPANXN2; NbExp=3; IntAct=EBI-297993, EBI-12023934;
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol {ECO:0000269|PubMed:18984161}.
CC Nucleus {ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:26912367,
CC ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770,
CC ECO:0000269|PubMed:28781166}. Note=SMN-mediated assembly into core
CC snRNPs occurs in the cytosol before SMN-mediated transport to the
CC nucleus to be included in spliceosomes. {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=P62316-1; Sequence=Displayed;
CC Name=2;
CC IsoId=P62316-2; Sequence=VSP_045371;
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; U15008; AAC13776.1; -; mRNA.
DR EMBL; AK291912; BAF84601.1; -; mRNA.
DR EMBL; AC007191; AAD22673.1; -; Genomic_DNA.
DR EMBL; CH471126; EAW57373.1; -; Genomic_DNA.
DR EMBL; CH471126; EAW57374.1; -; Genomic_DNA.
DR EMBL; BC000486; AAH00486.1; -; mRNA.
DR EMBL; BC001930; AAH01930.1; -; mRNA.
DR EMBL; BU531743; -; NOT_ANNOTATED_CDS; mRNA.
DR CCDS; CCDS33053.1; -. [P62316-1]
DR CCDS; CCDS54281.1; -. [P62316-2]
DR PIR; I38861; I38861.
DR RefSeq; NP_004588.1; NM_004597.6. [P62316-1]
DR RefSeq; NP_808210.2; NM_177542.3. [P62316-2]
DR PDB; 1B34; X-ray; 2.50 A; B=1-118.
DR PDB; 3CW1; X-ray; 5.49 A; C/P/Q/R=1-118.
DR PDB; 3JCR; EM; 7.00 A; Q/q=1-118.
DR PDB; 3PGW; X-ray; 4.40 A; V/Y=1-118.
DR PDB; 4F7U; X-ray; 1.90 A; B/D=1-118.
DR PDB; 4PJO; X-ray; 3.30 A; D/R/d/r=1-118.
DR PDB; 4V98; X-ray; 3.10 A; AB/AJ/AR/AZ/Ah/Ap/Ax/BB/BJ/BR/BZ/Bh/Bp/Bx/CB/CJ/CR/CZ/Ch/Cp=1-118.
DR PDB; 4WZJ; X-ray; 3.60 A; AC/AJ/AQ/BC/BJ/BQ/CC/CJ/CQ/DC/DJ/DQ=1-118.
DR PDB; 5MQF; EM; 5.90 A; a/h=1-118.
DR PDB; 5O9Z; EM; 4.50 A; S/a/h=1-118.
DR PDB; 5XJC; EM; 3.60 A; d/k=1-118.
DR PDB; 5XJL; X-ray; 2.50 A; B=1-118.
DR PDB; 5XJQ; X-ray; 3.28 A; B=1-118.
DR PDB; 5XJR; X-ray; 3.12 A; B=1-118.
DR PDB; 5XJS; X-ray; 3.38 A; B=1-118.
DR PDB; 5XJT; X-ray; 2.92 A; B=1-118.
DR PDB; 5XJU; X-ray; 2.58 A; B=1-118.
DR PDB; 5YZG; EM; 4.10 A; d/k=1-118.
DR PDB; 5Z56; EM; 5.10 A; d/k=1-118.
DR PDB; 5Z57; EM; 6.50 A; d/k=1-118.
DR PDB; 5Z58; EM; 4.90 A; d/k=1-118.
DR PDB; 6AH0; EM; 5.70 A; P/a/k=1-118.
DR PDB; 6AHD; EM; 3.80 A; P/c/k=1-118.
DR PDB; 6FF7; EM; 4.50 A; a/h=1-118.
DR PDB; 6ICZ; EM; 3.00 A; d/k=1-118.
DR PDB; 6ID0; EM; 2.90 A; d/k=1-118.
DR PDB; 6ID1; EM; 2.86 A; d/k=1-118.
DR PDB; 6QDV; EM; 3.30 A; j/m=1-118.
DR PDB; 6QW6; EM; 2.92 A; 42/52=1-118.
DR PDB; 6QX9; EM; 3.28 A; 12/22/42/52=1-118.
DR PDB; 6Y53; EM; 7.10 A; h=1-118.
DR PDB; 6Y5Q; EM; 7.10 A; h=1-118.
DR PDB; 7A5P; EM; 5.00 A; d/h=1-118.
DR PDB; 7ABG; EM; 7.80 A; a/h=1-118.
DR PDB; 7ABI; EM; 8.00 A; a/h=1-118.
DR PDB; 7B0Y; EM; 3.60 A; e=1-118.
DR PDB; 7DVQ; EM; 2.89 A; d/k=1-118.
DR PDBsum; 1B34; -.
DR PDBsum; 3CW1; -.
DR PDBsum; 3JCR; -.
DR PDBsum; 3PGW; -.
DR PDBsum; 4F7U; -.
DR PDBsum; 4PJO; -.
DR PDBsum; 4V98; -.
DR PDBsum; 4WZJ; -.
DR PDBsum; 5MQF; -.
DR PDBsum; 5O9Z; -.
DR PDBsum; 5XJC; -.
DR PDBsum; 5XJL; -.
DR PDBsum; 5XJQ; -.
DR PDBsum; 5XJR; -.
DR PDBsum; 5XJS; -.
DR PDBsum; 5XJT; -.
DR PDBsum; 5XJU; -.
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; 6Y53; -.
DR PDBsum; 6Y5Q; -.
DR PDBsum; 7A5P; -.
DR PDBsum; 7ABG; -.
DR PDBsum; 7ABI; -.
DR PDBsum; 7B0Y; -.
DR PDBsum; 7DVQ; -.
DR AlphaFoldDB; P62316; -.
DR SMR; P62316; -.
DR BioGRID; 112517; 230.
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; P62316; -.
DR DIP; DIP-31219N; -.
DR IntAct; P62316; 106.
DR MINT; P62316; -.
DR STRING; 9606.ENSP00000342374; -.
DR DrugBank; DB11638; Artenimol.
DR GlyGen; P62316; 1 site, 1 O-linked glycan (1 site).
DR iPTMnet; P62316; -.
DR MetOSite; P62316; -.
DR PhosphoSitePlus; P62316; -.
DR SwissPalm; P62316; -.
DR BioMuta; SNRPD2; -.
DR DMDM; 51338666; -.
DR EPD; P62316; -.
DR jPOST; P62316; -.
DR MassIVE; P62316; -.
DR MaxQB; P62316; -.
DR PaxDb; P62316; -.
DR PeptideAtlas; P62316; -.
DR PRIDE; P62316; -.
DR ProteomicsDB; 57392; -. [P62316-1]
DR TopDownProteomics; P62316-1; -. [P62316-1]
DR TopDownProteomics; P62316-2; -. [P62316-2]
DR ABCD; P62316; 7 sequenced antibodies.
DR Antibodypedia; 31375; 207 antibodies from 27 providers.
DR DNASU; 6633; -.
DR Ensembl; ENST00000342669.8; ENSP00000342374.2; ENSG00000125743.11. [P62316-1]
DR Ensembl; ENST00000391932.7; ENSP00000375798.2; ENSG00000125743.11. [P62316-2]
DR Ensembl; ENST00000587367.5; ENSP00000465952.1; ENSG00000125743.11. [P62316-2]
DR Ensembl; ENST00000588301.5; ENSP00000465216.1; ENSG00000125743.11. [P62316-1]
DR Ensembl; ENST00000588599.5; ENSP00000466152.1; ENSG00000125743.11. [P62316-2]
DR GeneID; 6633; -.
DR KEGG; hsa:6633; -.
DR MANE-Select; ENST00000342669.8; ENSP00000342374.2; NM_001384647.1; NP_001371576.1.
DR UCSC; uc002pcv.4; human. [P62316-1]
DR CTD; 6633; -.
DR DisGeNET; 6633; -.
DR GeneCards; SNRPD2; -.
DR HGNC; HGNC:11159; SNRPD2.
DR HPA; ENSG00000125743; Low tissue specificity.
DR MIM; 601061; gene.
DR neXtProt; NX_P62316; -.
DR OpenTargets; ENSG00000125743; -.
DR PharmGKB; PA36000; -.
DR VEuPathDB; HostDB:ENSG00000125743; -.
DR eggNOG; KOG3459; Eukaryota.
DR GeneTree; ENSGT00390000017608; -.
DR HOGENOM; CLU_076902_2_1_1; -.
DR InParanoid; P62316; -.
DR OMA; PKTEMSQ; -.
DR OrthoDB; 1581611at2759; -.
DR PhylomeDB; P62316; -.
DR TreeFam; TF319595; -.
DR PathwayCommons; P62316; -.
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-9754678; SARS-CoV-2 modulates host translation machinery.
DR SignaLink; P62316; -.
DR BioGRID-ORCS; 6633; 797 hits in 1051 CRISPR screens.
DR ChiTaRS; SNRPD2; human.
DR EvolutionaryTrace; P62316; -.
DR GenomeRNAi; 6633; -.
DR Pharos; P62316; Tbio.
DR PRO; PR:P62316; -.
DR Proteomes; UP000005640; Chromosome 19.
DR RNAct; P62316; protein.
DR Bgee; ENSG00000125743; Expressed in adult organism and 210 other tissues.
DR ExpressionAtlas; P62316; baseline and differential.
DR Genevisible; P62316; HS.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; IDA:UniProtKB.
DR GO; GO:0005829; C:cytosol; IDA:UniProtKB.
DR GO; GO:0070062; C:extracellular exosome; HDA:UniProtKB.
DR GO; GO:0034709; C:methylosome; IDA:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
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: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:0003723; F:RNA binding; HDA:UniProtKB.
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:0008380; P:RNA splicing; TAS:ProtInc.
DR GO; GO:0000245; P:spliceosomal complex assembly; 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; cd01720; Sm_D2; 1.
DR IDEAL; IID00160; -.
DR InterPro; IPR001163; LSM_dom_euk/arc.
DR InterPro; IPR010920; LSM_dom_sf.
DR InterPro; IPR027248; Sm_D2.
DR PANTHER; PTHR12777; PTHR12777; 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; Isopeptide bond; mRNA processing; mRNA splicing;
KW Nucleus; Phosphoprotein; Reference proteome; Ribonucleoprotein;
KW Spliceosome; Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|Ref.6, ECO:0007744|PubMed:22814378,
FT ECO:0007744|PubMed:25944712"
FT CHAIN 2..118
FT /note="Small nuclear ribonucleoprotein Sm D2"
FT /id="PRO_0000122207"
FT REGION 1..31
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 11..25
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0000269|Ref.6, ECO:0007744|PubMed:22814378,
FT ECO:0007744|PubMed:25944712"
FT MOD_RES 9
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT MOD_RES 12
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:20068231,
FT ECO:0007744|PubMed:23186163"
FT CROSSLNK 6
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT CROSSLNK 8
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT VAR_SEQ 1..10
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:15489334"
FT /id="VSP_045371"
FT CONFLICT 38
FT /note="N -> S (in Ref. 5; BU531743)"
FT /evidence="ECO:0000305"
FT HELIX 15..17
FT /evidence="ECO:0007829|PDB:5XJQ"
FT HELIX 18..22
FT /evidence="ECO:0007829|PDB:5XJQ"
FT TURN 23..25
FT /evidence="ECO:0007829|PDB:5XJL"
FT HELIX 28..38
FT /evidence="ECO:0007829|PDB:1B34"
FT STRAND 41..46
FT /evidence="ECO:0007829|PDB:1B34"
FT TURN 47..49
FT /evidence="ECO:0007829|PDB:5XJQ"
FT STRAND 51..59
FT /evidence="ECO:0007829|PDB:1B34"
FT STRAND 65..73
FT /evidence="ECO:0007829|PDB:1B34"
FT STRAND 83..85
FT /evidence="ECO:0007829|PDB:6ID1"
FT STRAND 94..101
FT /evidence="ECO:0007829|PDB:1B34"
FT HELIX 103..105
FT /evidence="ECO:0007829|PDB:1B34"
FT STRAND 106..111
FT /evidence="ECO:0007829|PDB:1B34"
SQ SEQUENCE 118 AA; 13527 MW; D986059D82B7E045 CRC64;
MSLLNKPKSE MTPEELQKRE EEEFNTGPLS VLTQSVKNNT QVLINCRNNK KLLGRVKAFD
RHCNMVLENV KEMWTEVPKS GKGKKKSKPV NKDRYISKMF LRGDSVIVVL RNPLIAGK
