SMD1_YEAST
ID SMD1_YEAST Reviewed; 146 AA.
AC Q02260; D6VUK6;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1993, sequence version 1.
DT 03-AUG-2022, entry version 188.
DE RecName: Full=Small nuclear ribonucleoprotein Sm D1;
DE Short=Sm-D1;
DE AltName: Full=snRNP core protein D1;
GN Name=SMD1; OrderedLocusNames=YGR074W;
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], AND FUNCTION.
RC STRAIN=S288c / GRF88;
RX PubMed=8430095; DOI=10.1073/pnas.90.3.848;
RA Rymond B.C.;
RT "Convergent transcripts of the yeast PRP38-SMD1 locus encode two essential
RT splicing factors, including the D1 core polypeptide of small nuclear
RT ribonucleoprotein particles.";
RL Proc. Natl. Acad. Sci. U.S.A. 90:848-852(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
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 [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND 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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169869;
RA Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J.,
RA Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M.,
RA Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L.,
RA Coblenz A., Coglievina M., Coissac E., Defoor E., Del Bino S., Delius H.,
RA Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P.,
RA Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M.,
RA Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A.,
RA Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K.,
RA Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P.,
RA Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E.,
RA Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
RA Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A.,
RA Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S.,
RA Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M.,
RA Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C.,
RA Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M.,
RA Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M.,
RA Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y.,
RA Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L.,
RA Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D.,
RA Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F.,
RA Zaccaria P., Zimmermann M., Zollner A., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
RL Nature 387:81-84(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 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 [10]
RP NUCLEAR LOCALIZATION SIGNAL.
RX PubMed=11027265; DOI=10.1128/mcb.20.21.7943-7954.2000;
RA Bordonne R.;
RT "Functional characterization of nuclear localization signals in yeast Sm
RT proteins.";
RL Mol. Cell. Biol. 20:7943-7954(2000).
RN [11]
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 [12]
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 [13]
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 [14]
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).
RN [15]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
CC -!- FUNCTION: lays 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:8430095). Also
CC binds telomerase RNA and is required for its accumulation
CC (PubMed:10490028). {ECO:0000269|PubMed:10490028,
CC ECO:0000269|PubMed:8430095}.
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. Belongs to
CC the CWC complex (or CEF1-associated complex), a spliceosome sub-complex
CC reminiscent of a late-stage spliceosome composed of the U2, U5 and U6
CC snRNAs and at least BUD13, BUD31, BRR2, CDC40, CEF1, CLF1, CUS1, CWC2,
CC CWC15, CWC21, CWC22, CWC23, CWC24, CWC25, CWC27, ECM2, HSH155, IST3,
CC ISY1, LEA1, MSL1, NTC20, PRP8, PRP9, PRP11, PRP19, PRP21, PRP22, PRP45,
CC PRP46, SLU7, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, SNT309, SNU114, SPP2,
CC SYF1, SYF2, RSE1 and YJU2. Component of the U4/U6-U5 tri-snRNP complex
CC composed of the U4, U6 and U5 snRNAs and at least PRP3, PRP4, PRP6,
CC PRP8, PRP18, PRP31, PRP38, SNU13, SNU23, SNU66, SNU114, SPP381, SMB1,
CC SMD1, SMD2, SMD3, SMX2, SMX3, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, LSM8,
CC BRR2 and DIB1. {ECO:0000269|PubMed:10449419,
CC ECO:0000269|PubMed:11302706, ECO:0000269|PubMed:11884590}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:O42661}. Cytoplasm
CC {ECO:0000250|UniProtKB:O42661}.
CC -!- DOMAIN: C-terminal extension may function as a nuclear localization
CC signal (NLS).
CC -!- MISCELLANEOUS: Present with 2400 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the snRNP core protein family. {ECO:0000305}.
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DR EMBL; L04669; AAA35055.1; -; Genomic_DNA.
DR EMBL; Z72858; CAA97076.1; -; Genomic_DNA.
DR EMBL; AY692847; AAT92866.1; -; Genomic_DNA.
DR EMBL; BK006941; DAA08167.1; -; Genomic_DNA.
DR PIR; A47264; A47264.
DR RefSeq; NP_011588.3; NM_001181203.3.
DR PDB; 3JCM; EM; 3.80 A; P/T=1-146.
DR PDB; 5GAM; EM; 3.70 A; h=1-146.
DR PDB; 5GAN; EM; 3.60 A; h/l=1-146.
DR PDB; 5GAO; EM; 3.60 A; l=1-146.
DR PDB; 5GM6; EM; 3.50 A; m=1-146.
DR PDB; 5GMK; EM; 3.40 A; m/z=1-146.
DR PDB; 5LJ3; EM; 3.80 A; h/l=1-146.
DR PDB; 5LJ5; EM; 3.80 A; h/l=1-146.
DR PDB; 5LQW; EM; 5.80 A; h=1-146.
DR PDB; 5MPS; EM; 3.85 A; h=1-146.
DR PDB; 5MQ0; EM; 4.17 A; h/l=1-146.
DR PDB; 5NRL; EM; 7.20 A; h/l/t=1-146.
DR PDB; 5WSG; EM; 4.00 A; V/m=1-146.
DR PDB; 5Y88; EM; 3.70 A; f/m=1-146.
DR PDB; 5YLZ; EM; 3.60 A; f/m=1-146.
DR PDB; 5ZWM; EM; 3.40 A; Q/b/m=1-146.
DR PDB; 5ZWN; EM; 3.30 A; b=1-146.
DR PDB; 5ZWO; EM; 3.90 A; Q/b/m=1-146.
DR PDB; 6BK8; EM; 3.30 A; h/p=1-146.
DR PDB; 6EXN; EM; 3.70 A; h/l=1-146.
DR PDB; 6G90; EM; 4.00 A; h/t=1-146.
DR PDB; 6J6G; EM; 3.20 A; m/z=1-146.
DR PDB; 6J6H; EM; 3.60 A; m/z=1-146.
DR PDB; 6J6N; EM; 3.86 A; m/z=1-146.
DR PDB; 6J6Q; EM; 3.70 A; m/z=1-146.
DR PDB; 6N7P; EM; 3.60 A; L=1-146.
DR PDB; 6N7R; EM; 3.20 A; L=1-146.
DR PDB; 6N7X; EM; 3.60 A; L=1-146.
DR PDB; 7B9V; EM; 2.80 A; h/l=1-146.
DR PDB; 7OQB; EM; 9.00 A; t=1-146.
DR PDB; 7OQC; EM; 4.10 A; h=1-146.
DR PDB; 7OQE; EM; 5.90 A; h/t=1-146.
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; Q02260; -.
DR SMR; Q02260; -.
DR BioGRID; 33316; 386.
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-227N; -.
DR IntAct; Q02260; 27.
DR MINT; Q02260; -.
DR STRING; 4932.YGR074W; -.
DR MaxQB; Q02260; -.
DR PaxDb; Q02260; -.
DR PRIDE; Q02260; -.
DR EnsemblFungi; YGR074W_mRNA; YGR074W; YGR074W.
DR GeneID; 852964; -.
DR KEGG; sce:YGR074W; -.
DR SGD; S000003306; SMD1.
DR VEuPathDB; FungiDB:YGR074W; -.
DR eggNOG; KOG3428; Eukaryota.
DR HOGENOM; CLU_123956_2_0_1; -.
DR InParanoid; Q02260; -.
DR OMA; WGTLQTV; -.
DR BioCyc; YEAST:G3O-30786-MON; -.
DR PRO; PR:Q02260; -.
DR Proteomes; UP000002311; Chromosome VII.
DR RNAct; Q02260; 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; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
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:0030532; C:small nuclear ribonucleoprotein complex; IMP:UniProtKB.
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; IMP:UniProtKB.
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 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; Cytoplasm; Direct protein sequencing; mRNA processing;
KW mRNA splicing; Nucleus; Reference proteome; Ribonucleoprotein; RNA-binding.
FT CHAIN 1..146
FT /note="Small nuclear ribonucleoprotein Sm D1"
FT /id="PRO_0000122206"
FT REGION 118..146
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 128..144
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255"
FT HELIX 4..7
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 14..19
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 24..32
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 38..46
FT /evidence="ECO:0007829|PDB:6J6G"
FT TURN 52..54
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 59..66
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 76..83
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 85..87
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 89..91
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 92..96
FT /evidence="ECO:0007829|PDB:6J6G"
FT STRAND 99..101
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 103..106
FT /evidence="ECO:0007829|PDB:6J6G"
FT HELIX 110..118
FT /evidence="ECO:0007829|PDB:6J6G"
SQ SEQUENCE 146 AA; 16275 MW; 9929F21EB9218447 CRC64;
MKLVNFLKKL RNEQVTIELK NGTTVWGTLQ SVSPQMNAIL TDVKLTLPQP RLNKLNSNGI
AMASLYLTGG QQPTASDNIA SLQYINIRGN TIRQIILPDS LNLDSLLVDQ KQLNSLRRSG
QIANDPSKKR RRDFGAPANK RPRRGL
