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Small nuclear ribonucleoprotein Sm D1 (Sm-D1) (snRNP core protein D1)

 SMD1_YEAST              Reviewed;         146 AA.
Q02260; D6VUK6;
01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
01-OCT-1993, sequence version 1.
22-NOV-2017, entry version 155.
RecName: Full=Small nuclear ribonucleoprotein Sm D1;
Short=Sm-D1;
AltName: Full=snRNP core protein D1;
Name=SMD1; OrderedLocusNames=YGR074W;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
STRAIN=S288c / GRF88;
PubMed=8430095; DOI=10.1073/pnas.90.3.848;
Rymond B.C.;
"Convergent transcripts of the yeast PRP38-SMD1 locus encode two
essential splicing factors, including the D1 core polypeptide of small
nuclear ribonucleoprotein particles.";
Proc. Natl. Acad. Sci. U.S.A. 90:848-852(1993).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=9528767; DOI=10.1128/MCB.18.4.1956;
Camasses A., Bragado-Nilsson E., Martin R., Seraphin B., Bordonne R.;
"Interactions within the yeast Sm core complex: from proteins to amino
acids.";
Mol. Cell. Biol. 18:1956-1966(1998).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND RNA-BINDING.
PubMed=10369684; DOI=10.1093/emboj/18.12.3451;
Salgado-Garrido J., Bragado-Nilsson E., Kandels-Lewis S., Seraphin B.;
"Sm and Sm-like proteins assemble in two related complexes of deep
evolutionary origin.";
EMBO J. 18:3451-3462(1999).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
PubMed=10490028; DOI=10.1038/43694;
Seto A.G., Zaug A.J., Sobel S.G., Wolin S.L., Cech T.R.;
"Saccharomyces cerevisiae telomerase is an Sm small nuclear
ribonucleoprotein particle.";
Nature 401:177-180(1999).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169869;
Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M.,
Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J.,
Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E.,
Clemente M.L., Coblenz A., Coglievina M., Coissac E., Defoor E.,
Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B.,
Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L.,
Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M.,
Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M.,
Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B.,
Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W.,
Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A.,
Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S.,
Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L.,
Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S.,
Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J.,
Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M.,
Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B.,
Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J.,
Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M.,
van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M.,
Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H.,
Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M.,
Zollner A., Kleine K.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
Nature 387:81-84(1997).
[6]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[7]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=17322287; DOI=10.1101/gr.6037607;
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A.,
Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F.,
Williamson J., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G.,
Kolodner R.D., LaBaer J.;
"Approaching a complete repository of sequence-verified protein-
encoding clones for Saccharomyces cerevisiae.";
Genome Res. 17:536-543(2007).
[8]
PARTIAL PROTEIN SEQUENCE.
PubMed=9012791; DOI=10.1073/pnas.94.2.385;
Neubauer G., Gottschalk A., Fabrizio P., Seraphin B., Luehrmann R.,
Mann M.;
"Identification of the proteins of the yeast U1 small nuclear
ribonucleoprotein complex by mass spectrometry.";
Proc. Natl. Acad. Sci. U.S.A. 94:385-390(1997).
[9]
SUBUNIT, IDENTIFICATION IN THE U4/U5/U6 TRI-SNRNP COMPLEX, AND
IDENTIFICATION BY MASS SPECTROMETRY.
PubMed=10449419; DOI=10.1093/emboj/18.16.4535;
Gottschalk A., Neubauer G., Banroques J., Mann M., Luehrmann R.,
Fabrizio P.;
"Identification by mass spectrometry and functional analysis of novel
proteins of the yeast [U4/U6.U5] tri-snRNP.";
EMBO J. 18:4535-4548(1999).
[10]
NUCLEAR LOCALIZATION SIGNAL.
PubMed=11027265; DOI=10.1128/MCB.20.21.7943-7954.2000;
Bordonne R.;
"Functional characterization of nuclear localization signals in yeast
Sm proteins.";
Mol. Cell. Biol. 20:7943-7954(2000).
[11]
SUBUNIT.
PubMed=11302706; DOI=10.1006/jmbi.2001.4549;
Walke S., Bragado-Nilsson E., Seraphin B., Nagai K.;
"Stoichiometry of the Sm proteins in yeast spliceosomal snRNPs
supports the heptamer ring model of the core domain.";
J. Mol. Biol. 308:49-58(2001).
[12]
CHARACTERIZATION OF THE SPLICEOSOME.
PubMed=11804584; DOI=10.1016/S1097-2765(02)00436-7;
Stevens S.W., Ryan D.E., Ge H.Y., Moore R.E., Young M.K., Lee T.D.,
Abelson J.;
"Composition and functional characterization of the yeast spliceosomal
penta-snRNP.";
Mol. Cell 9:31-44(2002).
[13]
IDENTIFICATION IN THE CWC COMPLEX, AND IDENTIFICATION BY MASS
SPECTROMETRY.
PubMed=11884590; DOI=10.1128/MCB.22.7.2011-2024.2002;
Ohi M.D., Link A.J., Ren L., Jennings J.L., McDonald W.H., Gould K.L.;
"Proteomics analysis reveals stable multiprotein complexes in both
fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel
pre-mRNA splicing factors, and snRNAs.";
Mol. Cell. Biol. 22:2011-2024(2002).
[14]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
-!- FUNCTION: Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4
and U5 which contain a highly conserved structural motif called
the Sm binding site. Also binds telomerase RNA and is required for
its accumulation. {ECO:0000269|PubMed:10490028,
ECO:0000269|PubMed:8430095}.
-!- SUBUNIT: Component of the Sm core complex, present in spliceosomal
snRNP U1, U2, U4/U6 and U5. The core complex contains SMB1, SMD1,
SMD2, SMD3, SME1, SMX3 and SMX2 (Sm proteins B, D1, D2, D3, E, F
and G, respectively), and is probably a heptameric ring structure.
Belongs to the CWC complex (or CEF1-associated complex), a
spliceosome sub-complex reminiscent of a late-stage spliceosome
composed of the U2, U5 and U6 snRNAs and at least BUD13, BUD31,
BRR2, CDC40, CEF1, CLF1, CUS1, CWC2, CWC15, CWC21, CWC22, CWC23,
CWC24, CWC25, CWC27, ECM2, HSH155, IST3, ISY1, LEA1, MSL1, NTC20,
PRP8, PRP9, PRP11, PRP19, PRP21, PRP22, PRP45, PRP46, SLU7, SMB1,
SMD1, SMD2, SMD3, SMX2, SMX3, SNT309, SNU114, SPP2, SYF1, SYF2,
RSE1 and YJU2. Component of the U4/U6-U5 tri-snRNP complex
composed of the U4, U6 and U5 snRNAs and at least PRP3, PRP4,
PRP6, PRP8, PRP18, PRP31, PRP38, SNU13, SNU23, SNU66, SNU114,
SPP381, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, LSM2, LSM3, LSM4,
LSM5, LSM6, LSM7, LSM8, BRR2 and DIB1.
{ECO:0000269|PubMed:10449419, ECO:0000269|PubMed:11302706,
ECO:0000269|PubMed:11884590}.
-!- SUBCELLULAR LOCATION: Nucleus.
-!- DOMAIN: C-terminal extension may function as a nuclear
localization signal (NLS).
-!- MISCELLANEOUS: Present with 2400 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the snRNP core protein family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; L04669; AAA35055.1; -; Genomic_DNA.
EMBL; Z72858; CAA97076.1; -; Genomic_DNA.
EMBL; AY692847; AAT92866.1; -; Genomic_DNA.
EMBL; BK006941; DAA08167.1; -; Genomic_DNA.
PIR; A47264; A47264.
RefSeq; NP_011588.3; NM_001181203.3.
PDB; 3JCM; EM; 3.80 A; P/T=1-146.
PDB; 5GAM; EM; 3.70 A; h=1-146.
PDB; 5GAN; EM; 3.60 A; h/l=1-146.
PDB; 5GAO; EM; 3.60 A; l=1-146.
PDB; 5GM6; EM; 3.50 A; m=1-146.
PDB; 5GMK; EM; 3.40 A; m/z=1-146.
PDB; 5LJ3; EM; 3.80 A; h/l=1-146.
PDB; 5LJ5; EM; 3.80 A; h/l=1-146.
PDB; 5LQW; EM; 5.80 A; h=1-146.
PDB; 5MPS; EM; 3.85 A; h=1-146.
PDB; 5MQ0; EM; 4.17 A; h/l=1-146.
PDB; 5NRL; EM; 7.20 A; h/l/t=1-146.
PDB; 5WSG; EM; 4.00 A; V/m=1-146.
PDBsum; 3JCM; -.
PDBsum; 5GAM; -.
PDBsum; 5GAN; -.
PDBsum; 5GAO; -.
PDBsum; 5GM6; -.
PDBsum; 5GMK; -.
PDBsum; 5LJ3; -.
PDBsum; 5LJ5; -.
PDBsum; 5LQW; -.
PDBsum; 5MPS; -.
PDBsum; 5MQ0; -.
PDBsum; 5NRL; -.
PDBsum; 5WSG; -.
ProteinModelPortal; Q02260; -.
SMR; Q02260; -.
BioGrid; 33316; 377.
DIP; DIP-227N; -.
IntAct; Q02260; 26.
MINT; MINT-505581; -.
STRING; 4932.YGR074W; -.
MaxQB; Q02260; -.
PRIDE; Q02260; -.
EnsemblFungi; YGR074W; YGR074W; YGR074W.
GeneID; 852964; -.
KEGG; sce:YGR074W; -.
EuPathDB; FungiDB:YGR074W; -.
SGD; S000003306; SMD1.
GeneTree; ENSGT00510000047245; -.
HOGENOM; HOG000182713; -.
InParanoid; Q02260; -.
KO; K11087; -.
OMA; TVSPQMN; -.
OrthoDB; EOG092C5VL3; -.
BioCyc; YEAST:G3O-30786-MONOMER; -.
Reactome; R-SCE-72165; mRNA Splicing - Minor Pathway.
PRO; PR:Q02260; -.
Proteomes; UP000002311; Chromosome VII.
GO; GO:0071013; C:catalytic step 2 spliceosome; IBA:GO_Central.
GO; GO:0000243; C:commitment complex; IPI:SGD.
GO; GO:0005829; C:cytosol; IDA:SGD.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0034715; C:pICln-Sm protein complex; IBA:GO_Central.
GO; GO:0071011; C:precatalytic spliceosome; IBA:GO_Central.
GO; GO:0030532; C:small nuclear ribonucleoprotein complex; IMP:UniProtKB.
GO; GO:0034719; C:SMN-Sm protein complex; IBA:GO_Central.
GO; GO:0005685; C:U1 snRNP; IDA:SGD.
GO; GO:0005689; C:U12-type spliceosomal complex; IBA:GO_Central.
GO; GO:0005686; C:U2 snRNP; IBA:GO_Central.
GO; GO:0071004; C:U2-type prespliceosome; IDA:SGD.
GO; GO:0005687; C:U4 snRNP; IBA:GO_Central.
GO; GO:0046540; C:U4/U6 x U5 tri-snRNP complex; IDA:SGD.
GO; GO:0005682; C:U5 snRNP; IDA:SGD.
GO; GO:0003729; F:mRNA binding; IPI:SGD.
GO; GO:0000398; P:mRNA splicing, via spliceosome; IMP:UniProtKB.
GO; GO:0000245; P:spliceosomal complex assembly; IBA:GO_Central.
GO; GO:0000387; P:spliceosomal snRNP assembly; IBA:GO_Central.
CDD; cd01724; Sm_D1; 1.
InterPro; IPR027141; LSm4/Sm_D1/D3.
InterPro; IPR001163; LSM_dom_euk/arc.
InterPro; IPR010920; LSM_dom_sf.
InterPro; IPR034102; Sm_D1.
PANTHER; PTHR23338; PTHR23338; 1.
Pfam; PF01423; LSM; 1.
SMART; SM00651; Sm; 1.
SUPFAM; SSF50182; SSF50182; 2.
1: Evidence at protein level;
3D-structure; Complete proteome; Direct protein sequencing;
mRNA processing; mRNA splicing; Nucleus; Reference proteome;
Ribonucleoprotein; RNA-binding.
CHAIN 1 146 Small nuclear ribonucleoprotein Sm D1.
/FTId=PRO_0000122206.
MOTIF 128 144 Nuclear localization signal.
{ECO:0000255}.
HELIX 3 9 {ECO:0000244|PDB:5GMK}.
STRAND 12 19 {ECO:0000244|PDB:5GMK}.
STRAND 24 32 {ECO:0000244|PDB:5GMK}.
STRAND 38 46 {ECO:0000244|PDB:5GMK}.
STRAND 80 87 {ECO:0000244|PDB:5GMK}.
TURN 89 91 {ECO:0000244|PDB:5GMK}.
STRAND 92 96 {ECO:0000244|PDB:5GMK}.
HELIX 103 107 {ECO:0000244|PDB:5GMK}.
SEQUENCE 146 AA; 16275 MW; 9929F21EB9218447 CRC64;
MKLVNFLKKL RNEQVTIELK NGTTVWGTLQ SVSPQMNAIL TDVKLTLPQP RLNKLNSNGI
AMASLYLTGG QQPTASDNIA SLQYINIRGN TIRQIILPDS LNLDSLLVDQ KQLNSLRRSG
QIANDPSKKR RRDFGAPANK RPRRGL


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