SMD3B_ARATH
ID SMD3B_ARATH Reviewed; 131 AA.
AC Q9LM92; Q8LC48; Q9LMW6;
DT 27-MAY-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 25-MAY-2022, entry version 132.
DE RecName: Full=Small nuclear ribonucleoprotein SmD3b {ECO:0000305};
DE Short=SmD3-b {ECO:0000303|PubMed:21421416};
DE AltName: Full=snRNP core protein D3-b {ECO:0000305};
GN Name=SMD3B {ECO:0000303|PubMed:21421416};
GN OrderedLocusNames=At1g20580 {ECO:0000312|Araport:AT1G20580};
GN ORFNames=F2D10.7 {ECO:0000312|EMBL:AAF80609.1},
GN F5M15.9 {ECO:0000312|EMBL:AAF79623.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, TISSUE SPECIFICITY, AND DISRUPTION PHENOTYPE.
RX PubMed=21421416; DOI=10.1016/j.plantsci.2011.01.011;
RA Swaraz A.M., Park Y.D., Hur Y.;
RT "Knock-out mutations of Arabidopsis SmD3-b induce pleotropic phenotypes
RT through altered transcript splicing.";
RL Plant Sci. 180:661-671(2011).
CC -!- FUNCTION: Core component of the spliceosomal U1, U2, U4 and U5 small
CC nuclear ribonucleoproteins (snRNPs), the building blocks of the
CC spliceosome (By similarity). May play a major role in the splicing of
CC cellular pre-mRNAs. Required for normal plant development
CC (PubMed:21421416). {ECO:0000250|UniProtKB:P62318,
CC ECO:0000269|PubMed:21421416}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm, cytosol
CC {ECO:0000250|UniProtKB:P62318}. Nucleus {ECO:0000250|UniProtKB:P62318}.
CC Note=SMN-mediated assembly into core snRNPs occurs in the cytosol
CC before SMN-mediated transport to the nucleus to be included in
CC spliceosomes. {ECO:0000250|UniProtKB:P62318}.
CC -!- TISSUE SPECIFICITY: Expressed in young seedlings, roots, leaves,
CC flowers and immature siliques. {ECO:0000269|PubMed:21421416}.
CC -!- DISRUPTION PHENOTYPE: Pleiotropic phenotypes of delayed flowering time
CC and seed production, reduced root growth, partially defective leaf
CC venation, abnormal numbers of trichome branches and changed numbers of
CC floral organs. The double mutants smd3-a and smd3-b display embryonic
CC lethality. {ECO:0000269|PubMed:21421416}.
CC -!- SIMILARITY: Belongs to the snRNP core protein family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF79623.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC027665; AAF79623.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC069251; AAF80609.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE29990.1; -; Genomic_DNA.
DR EMBL; AF412086; AAL06539.1; -; mRNA.
DR EMBL; AY093974; AAM16235.1; -; mRNA.
DR EMBL; AY086797; AAM63846.1; -; mRNA.
DR RefSeq; NP_564119.1; NM_101909.4.
DR AlphaFoldDB; Q9LM92; -.
DR SMR; Q9LM92; -.
DR IntAct; Q9LM92; 1.
DR STRING; 3702.AT1G20580.1; -.
DR PaxDb; Q9LM92; -.
DR PRIDE; Q9LM92; -.
DR ProteomicsDB; 234531; -.
DR EnsemblPlants; AT1G20580.1; AT1G20580.1; AT1G20580.
DR GeneID; 838647; -.
DR Gramene; AT1G20580.1; AT1G20580.1; AT1G20580.
DR KEGG; ath:AT1G20580; -.
DR Araport; AT1G20580; -.
DR TAIR; locus:2030442; AT1G20580.
DR eggNOG; KOG3172; Eukaryota.
DR HOGENOM; CLU_099537_1_0_1; -.
DR InParanoid; Q9LM92; -.
DR OMA; HMQEIIM; -.
DR OrthoDB; 1584810at2759; -.
DR PhylomeDB; Q9LM92; -.
DR PRO; PR:Q9LM92; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9LM92; baseline and differential.
DR Genevisible; Q9LM92; AT.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; IBA:GO_Central.
DR GO; GO:0000243; C:commitment complex; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IEA:UniProtKB-SubCell.
DR GO; GO:0005730; C:nucleolus; HDA:TAIR.
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:0097526; C:spliceosomal tri-snRNP complex; IBA:GO_Central.
DR GO; GO:0005685; C:U1 snRNP; IBA:GO_Central.
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:0005687; C:U4 snRNP; IBA:GO_Central.
DR GO; GO:0005682; C:U5 snRNP; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0048589; P:developmental growth; IMP:UniProtKB.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IMP:UniProtKB.
DR GO; GO:0000387; P:spliceosomal snRNP assembly; IBA:GO_Central.
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 2: Evidence at transcript level;
KW Cytoplasm; mRNA processing; mRNA splicing; Nucleus; Reference proteome;
KW Ribonucleoprotein; RNA-binding; Spliceosome.
FT CHAIN 1..131
FT /note="Small nuclear ribonucleoprotein SmD3b"
FT /id="PRO_0000433110"
FT REGION 96..131
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 106
FT /note="G -> A (in Ref. 4; AAM63846)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 131 AA; 14238 MW; 9A9A5E2D9F9E715C CRC64;
MSRSLGIPVK LLHEASGHIV TVELKSGELY RGSMIECEDN WNCQLEDITY TAKDGKVSQL
EHVFIRGSKV RFMVIPDILK HAPMFKRLDA RIKGKSSSLG VGRGRGAMRG KPAAGPGRGT
GGRGAVPPVR R
