SMD3_YEAST
ID SMD3_YEAST Reviewed; 101 AA.
AC P43321; D6VYE2; E9P8W3;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 03-AUG-2022, entry version 176.
DE RecName: Full=Small nuclear ribonucleoprotein Sm D3;
DE Short=Sm-D3;
DE AltName: Full=snRNP core protein D3;
GN Name=SMD3; OrderedLocusNames=YLR147C; ORFNames=L9634.6;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1944264; DOI=10.1128/mcb.11.12.5801-5812.1991;
RA Preston R., Manolson M.F., Becherer K., Weindnhammer E., Kirkpatrick D.,
RA Wright R., Jones E.W.;
RT "Isolation and characterization of PEP3, a gene required for vacuolar
RT biogenesis in Saccharomyces cerevisiae.";
RL Mol. Cell. Biol. 11:5801-5812(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1840635; DOI=10.1128/mcb.11.12.5813-5824.1991;
RA Robinson J.S., Graham T.R., Emr S.D.;
RT "A putative zinc finger protein, Saccharomyces cerevisiae Vps18p, affects
RT late Golgi functions required for vacuolar protein sorting and efficient
RT alpha-factor prohormone maturation.";
RL Mol. Cell. Biol. 11:5813-5824(1991).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND INTERACTION WITH SMB1.
RX PubMed=9528767; DOI=10.1128/mcb.18.4.1956;
RA Camasses A., Bragado-Nilsson E., Martin R., Seraphin B., Bordonne R.;
RT "Interactions within the yeast Sm core complex: from proteins to amino
RT acids.";
RL Mol. Cell. Biol. 18:1956-1966(1998).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND RNA-BINDING.
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(1997).
RN [6]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [8]
RP PARTIAL PROTEIN SEQUENCE.
RX PubMed=9012791; DOI=10.1073/pnas.94.2.385;
RA Neubauer G., Gottschalk A., Fabrizio P., Seraphin B., Luehrmann R.,
RA Mann M.;
RT "Identification of the proteins of the yeast U1 small nuclear
RT ribonucleoprotein complex by mass spectrometry.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:385-390(1997).
RN [9]
RP IDENTIFICATION.
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 [10]
RP IDENTIFICATION, FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=7799953; DOI=10.1128/mcb.15.1.445;
RA Roy J., Zheng B., Rymond B.C., Woolford J.L. Jr.;
RT "Structurally related but functionally distinct yeast Sm D core small
RT nuclear ribonucleoprotein particle proteins.";
RL Mol. Cell. Biol. 15:445-455(1995).
RN [11]
RP SUBUNIT, IDENTIFICATION IN THE U4/U5/U6 TRI-SNRNP COMPLEX, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=10449419; DOI=10.1093/emboj/18.16.4535;
RA Gottschalk A., Neubauer G., Banroques J., Mann M., Luehrmann R.,
RA Fabrizio P.;
RT "Identification by mass spectrometry and functional analysis of novel
RT proteins of the yeast [U4/U6.U5] tri-snRNP.";
RL EMBO J. 18:4535-4548(1999).
RN [12]
RP FUNCTION.
RX PubMed=10490028; DOI=10.1038/43694;
RA Seto A.G., Zaug A.J., Sobel S.G., Wolin S.L., Cech T.R.;
RT "Saccharomyces cerevisiae telomerase is an Sm small nuclear
RT ribonucleoprotein particle.";
RL Nature 401:177-180(1999).
RN [13]
RP SUBUNIT.
RX PubMed=11302706; DOI=10.1006/jmbi.2001.4549;
RA Walke S., Bragado-Nilsson E., Seraphin B., Nagai K.;
RT "Stoichiometry of the Sm proteins in yeast spliceosomal snRNPs supports the
RT heptamer ring model of the core domain.";
RL J. Mol. Biol. 308:49-58(2001).
RN [14]
RP CHARACTERIZATION OF THE SPLICEOSOME.
RX PubMed=11804584; DOI=10.1016/s1097-2765(02)00436-7;
RA Stevens S.W., Ryan D.E., Ge H.Y., Moore R.E., Young M.K., Lee T.D.,
RA Abelson J.;
RT "Composition and functional characterization of the yeast spliceosomal
RT penta-snRNP.";
RL Mol. Cell 9:31-44(2002).
RN [15]
RP IDENTIFICATION IN THE CWC COMPLEX, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=11884590; DOI=10.1128/mcb.22.7.2011-2024.2002;
RA Ohi M.D., Link A.J., Ren L., Jennings J.L., McDonald W.H., Gould K.L.;
RT "Proteomics analysis reveals stable multiprotein complexes in both fission
RT and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA
RT splicing factors, and snRNAs.";
RL Mol. Cell. Biol. 22:2011-2024(2002).
RN [16]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=14690591; DOI=10.1016/s1097-2765(03)00476-3;
RA Hazbun T.R., Malmstroem L., Anderson S., Graczyk B.J., Fox B., Riffle M.,
RA Sundin B.A., Aranda J.D., McDonald W.H., Chiu C.-H., Snydsman B.E.,
RA Bradley P., Muller E.G.D., Fields S., Baker D., Yates J.R. III, Davis T.N.;
RT "Assigning function to yeast proteins by integration of technologies.";
RL Mol. Cell 12:1353-1365(2003).
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. Also binds telomerase
CC RNA and is required for its accumulation. {ECO:0000269|PubMed:10490028,
CC ECO:0000269|PubMed:7799953}.
CC -!- SUBUNIT: Component of the Sm core complex, present in spliceosomal
CC snRNP U1, U2, U4/U6 and U5. The core complex contains SMB1, SMD1, SMD2,
CC SMD3, SME1, SMX3 and SMX2 (Sm proteins B, D1, D2, D3, E, F and G,
CC respectively), and is probably a heptameric ring structure. SMD3
CC specifically interacts with SMB1. Belongs to the CWC complex (or CEF1-
CC associated complex), a spliceosome sub-complex reminiscent of a late-
CC stage spliceosome composed of the U2, U5 and U6 snRNAs and at least
CC BUD13, BUD31, BRR2, CDC40, CEF1, CLF1, CUS1, CWC2, CWC15, CWC21, CWC22,
CC CWC23, CWC24, CWC25, CWC27, ECM2, HSH155, IST3, ISY1, LEA1, MSL1,
CC NTC20, PRP8, PRP9, PRP11, PRP19, PRP21, PRP22, PRP45, PRP46, SLU7,
CC SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, SNT309, SNU114, SPP2, SYF1, SYF2,
CC RSE1 and YJU2. Component of the U4/U6-U5 tri-snRNP complex composed of
CC the U4, U6 and U5 snRNAs and at least PRP3, PRP4, PRP6, PRP8, PRP18,
CC PRP31, PRP38, SNU13, SNU23, SNU66, SNU114, SPP381, SMB1, SMD1, SMD2,
CC SMD3, SMX2, SMX3, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, LSM8, BRR2 and
CC DIB1. {ECO:0000269|PubMed:10449419, ECO:0000269|PubMed:11302706,
CC ECO:0000269|PubMed:11884590, ECO:0000269|PubMed:9528767}.
CC -!- INTERACTION:
CC P43321; P40018: SMB1; NbExp=3; IntAct=EBI-529, EBI-432;
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol {ECO:0000269|PubMed:7799953}.
CC Nucleus {ECO:0000269|PubMed:7799953}.
CC -!- SIMILARITY: Belongs to the snRNP core protein family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; M65144; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; Z73319; CAA97719.1; -; Genomic_DNA.
DR EMBL; U53879; AAB82381.1; -; Genomic_DNA.
DR EMBL; AY558533; AAS56859.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09458.1; -; Genomic_DNA.
DR PIR; S29093; S29093.
DR RefSeq; NP_013248.1; NM_001182034.1.
DR PDB; 3JCM; EM; 3.80 A; J/R=1-101.
DR PDB; 5GAM; EM; 3.70 A; d=1-101.
DR PDB; 5GAN; EM; 3.60 A; d/n=1-101.
DR PDB; 5GAO; EM; 3.60 A; n=1-101.
DR PDB; 5GM6; EM; 3.50 A; l=1-101.
DR PDB; 5GMK; EM; 3.40 A; l/y=1-101.
DR PDB; 5LJ3; EM; 3.80 A; d/n=1-101.
DR PDB; 5LJ5; EM; 3.80 A; d/n=1-101.
DR PDB; 5LQW; EM; 5.80 A; d=1-101.
DR PDB; 5MPS; EM; 3.85 A; d=1-101.
DR PDB; 5MQ0; EM; 4.17 A; d/n=1-101.
DR PDB; 5NRL; EM; 7.20 A; d/n/v=1-101.
DR PDB; 5WSG; EM; 4.00 A; U/l=1-101.
DR PDB; 5Y88; EM; 3.70 A; e/l=1-101.
DR PDB; 5YLZ; EM; 3.60 A; e/l=1-101.
DR PDB; 5ZWM; EM; 3.40 A; S/d/l=1-101.
DR PDB; 5ZWN; EM; 3.30 A; d=1-101.
DR PDB; 5ZWO; EM; 3.90 A; S/d/l=1-101.
DR PDB; 6BK8; EM; 3.30 A; g/o=1-101.
DR PDB; 6EXN; EM; 3.70 A; d/n=1-101.
DR PDB; 6G90; EM; 4.00 A; d/v=1-101.
DR PDB; 6J6G; EM; 3.20 A; l/y=1-101.
DR PDB; 6J6H; EM; 3.60 A; l/y=1-101.
DR PDB; 6J6N; EM; 3.86 A; l/y=1-101.
DR PDB; 6J6Q; EM; 3.70 A; l/y=1-101.
DR PDB; 6N7P; EM; 3.60 A; N=1-101.
DR PDB; 6N7R; EM; 3.20 A; N=1-101.
DR PDB; 6N7X; EM; 3.60 A; N=1-101.
DR PDB; 7B9V; EM; 2.80 A; d/n=1-101.
DR PDB; 7OQB; EM; 9.00 A; v=1-101.
DR PDB; 7OQC; EM; 4.10 A; d=1-101.
DR PDB; 7OQE; EM; 5.90 A; d/v=1-101.
DR PDBsum; 3JCM; -.
DR PDBsum; 5GAM; -.
DR PDBsum; 5GAN; -.
DR PDBsum; 5GAO; -.
DR PDBsum; 5GM6; -.
DR PDBsum; 5GMK; -.
DR PDBsum; 5LJ3; -.
DR PDBsum; 5LJ5; -.
DR PDBsum; 5LQW; -.
DR PDBsum; 5MPS; -.
DR PDBsum; 5MQ0; -.
DR PDBsum; 5NRL; -.
DR PDBsum; 5WSG; -.
DR PDBsum; 5Y88; -.
DR PDBsum; 5YLZ; -.
DR PDBsum; 5ZWM; -.
DR PDBsum; 5ZWN; -.
DR PDBsum; 5ZWO; -.
DR PDBsum; 6BK8; -.
DR PDBsum; 6EXN; -.
DR PDBsum; 6G90; -.
DR PDBsum; 6J6G; -.
DR PDBsum; 6J6H; -.
DR PDBsum; 6J6N; -.
DR PDBsum; 6J6Q; -.
DR PDBsum; 6N7P; -.
DR PDBsum; 6N7R; -.
DR PDBsum; 6N7X; -.
DR PDBsum; 7B9V; -.
DR PDBsum; 7OQB; -.
DR PDBsum; 7OQC; -.
DR PDBsum; 7OQE; -.
DR AlphaFoldDB; P43321; -.
DR SMR; P43321; -.
DR BioGRID; 31416; 70.
DR ComplexPortal; CPX-1651; PRP19-associated complex.
DR ComplexPortal; CPX-23; U1 small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-25; U4/U6.U5 tri-small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-26; U2 small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-29; U5 small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-30; U5 small nuclear ribonucleoprotein complex, AAR2 variant.
DR ComplexPortal; CPX-31; U4 small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-32; U4/U6 small nuclear ribonucleoprotein complex.
DR ComplexPortal; CPX-43; Sm complex.
DR DIP; DIP-715N; -.
DR IntAct; P43321; 27.
DR MINT; P43321; -.
DR STRING; 4932.YLR147C; -.
DR MaxQB; P43321; -.
DR PaxDb; P43321; -.
DR PRIDE; P43321; -.
DR TopDownProteomics; P43321; -.
DR EnsemblFungi; YLR147C_mRNA; YLR147C; YLR147C.
DR GeneID; 850839; -.
DR KEGG; sce:YLR147C; -.
DR SGD; S000004137; SMD3.
DR VEuPathDB; FungiDB:YLR147C; -.
DR eggNOG; KOG3172; Eukaryota.
DR GeneTree; ENSGT00610000086153; -.
DR HOGENOM; CLU_099537_1_2_1; -.
DR InParanoid; P43321; -.
DR OMA; MNCQLRD; -.
DR BioCyc; YEAST:G3O-32283-MON; -.
DR PRO; PR:P43321; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; P43321; protein.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; IBA:GO_Central.
DR GO; GO:0000243; C:commitment complex; IPI:SGD.
DR GO; GO:0005737; C:cytoplasm; IC:ComplexPortal.
DR GO; GO:0005829; C:cytosol; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IC:ComplexPortal.
DR GO; GO:0034715; C:pICln-Sm protein complex; IBA:GO_Central.
DR GO; GO:0071011; C:precatalytic spliceosome; IBA:GO_Central.
DR GO; GO:0034719; C:SMN-Sm protein complex; IBA:GO_Central.
DR GO; GO:0005681; C:spliceosomal complex; IC:ComplexPortal.
DR GO; GO:0097526; C:spliceosomal tri-snRNP complex; IBA:GO_Central.
DR GO; GO:0005685; C:U1 snRNP; IDA:SGD.
DR GO; GO:0005689; C:U12-type spliceosomal complex; IBA:GO_Central.
DR GO; GO:0005686; C:U2 snRNP; IBA:GO_Central.
DR GO; GO:0071004; C:U2-type prespliceosome; IDA:SGD.
DR GO; GO:0005687; C:U4 snRNP; IPI:ComplexPortal.
DR GO; GO:0071001; C:U4/U6 snRNP; IC:ComplexPortal.
DR GO; GO:0046540; C:U4/U6 x U5 tri-snRNP complex; IDA:SGD.
DR GO; GO:0005682; C:U5 snRNP; IDA:SGD.
DR GO; GO:0003729; F:mRNA binding; IPI:SGD.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0036261; P:7-methylguanosine cap hypermethylation; IMP:ComplexPortal.
DR GO; GO:0000395; P:mRNA 5'-splice site recognition; IC:ComplexPortal.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IPI:SGD.
DR GO; GO:0000245; P:spliceosomal complex assembly; IC:ComplexPortal.
DR GO; GO:0000387; P:spliceosomal snRNP assembly; IBA:GO_Central.
DR GO; GO:1903241; P:U2-type prespliceosome assembly; IC:ComplexPortal.
DR CDD; cd01721; Sm_D3; 1.
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; Cytoplasm; Direct protein sequencing; mRNA processing;
KW mRNA splicing; Nucleus; Reference proteome; Ribonucleoprotein; RNA-binding.
FT CHAIN 1..101
FT /note="Small nuclear ribonucleoprotein Sm D3"
FT /id="PRO_0000122220"
FT CONFLICT 88
FT /note="S -> P (in Ref. 7; AAS56859)"
FT /evidence="ECO:0000305"
FT HELIX 6..14
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 19..23
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 28..35
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 42..50
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 52..54
FT /evidence="ECO:0007829|PDB:5GMK"
FT STRAND 56..64
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 66..68
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 69..73
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 76..80
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 82..84
FT /evidence="ECO:0007829|PDB:6J6G"
SQ SEQUENCE 101 AA; 11224 MW; BB02A56C5AD70CF2 CRC64;
MTMNGIPVKL LNEAQGHIVS LELTTGATYR GKLVESEDSM NVQLRDVIAT EPQGAVTHMD
QIFVRGSQIK FIVVPDLLKN APLFKKNSSR PMPPIRGPKR R
