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Protein

Small nuclear ribonucleoprotein Sm D3

Gene

Snrpd3

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. As part of the U7 snRNP it is involved in histone 3'-end processing.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-MMU-109688. Cleavage of Growing Transcript in the Termination Region.
R-MMU-111367. SLBP independent Processing of Histone Pre-mRNAs.
R-MMU-191859. snRNP Assembly.
R-MMU-72163. mRNA Splicing - Major Pathway.
R-MMU-72165. mRNA Splicing - Minor Pathway.
R-MMU-77588. SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs.

Names & Taxonomyi

Protein namesi
Recommended name:
Small nuclear ribonucleoprotein Sm D3
Short name:
Sm-D3
Alternative name(s):
snRNP core protein D3
Gene namesi
Name:Snrpd3
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 10

Organism-specific databases

MGIiMGI:1914582. Snrpd3.

Subcellular locationi

  • Cytoplasmcytosol By similarity
  • Nucleus By similarity

  • Note: SMN-mediated assembly into core snRNPs occurs in the cytosol before SMN-mediated transport to the nucleus to be included in spliceosomes.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 126125Small nuclear ribonucleoprotein Sm D3PRO_0000122215Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity

Post-translational modificationi

Methylated on arginine residues by PRMT5 and PRMT7; probable asymmetric dimethylation which is required for assembly and biogenesis of snRNPs.By similarity

Keywords - PTMi

Acetylation, Methylation

Proteomic databases

EPDiP62320.
MaxQBiP62320.
PaxDbiP62320.
PeptideAtlasiP62320.
PRIDEiP62320.

PTM databases

iPTMnetiP62320.
PhosphoSiteiP62320.
SwissPalmiP62320.

Expressioni

Gene expression databases

BgeeiP62320.
CleanExiMM_SNRPD3.
GenevisibleiP62320. MM.

Interactioni

Subunit structurei

U1 snRNP is for instance composed of the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP, and at least three U1 snRNP-specific proteins SNRNP70/U1-70K, SNRPA/U1-A and SNRPC/U1-C. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Component of the U7 snRNP complex, or U7 Sm protein core complex, at least composed of LSM10, LSM11, SNRPB, SNRPD3, SNRPE, SNRPF, SNRPG and U7 snRNA. Part of the SMN-Sm complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8, STRAP/UNRIP and the Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG; catalyzes core snRNPs assembly. Forms a 6S pICln-Sm complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP (By similarity).By similarity

GO - Molecular functioni

Protein-protein interaction databases

BioGridi212112. 2 interactions.
IntActiP62320. 5 interactions.
MINTiMINT-124943.
STRINGi10090.ENSMUSP00000020397.

Structurei

3D structure databases

ProteinModelPortaliP62320.
SMRiP62320. Positions 1-84.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati110 – 11121
Repeati112 – 11322
Repeati114 – 11523
Repeati116 – 11724
Repeati118 – 11925

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni110 – 119105 X 2 AA tandem repeats of [RM]-G

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi84 – 12643Arg/Lys-rich (basic)Add
BLAST

Sequence similaritiesi

Belongs to the snRNP core protein family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG3172. Eukaryota.
COG1958. LUCA.
GeneTreeiENSGT00610000086153.
HOGENOMiHOG000182712.
HOVERGENiHBG105305.
InParanoidiP62320.
KOiK11088.
OMAiEGHVVTC.
OrthoDBiEOG7VTDQF.
PhylomeDBiP62320.
TreeFamiTF354302.

Family and domain databases

InterProiIPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
[Graphical view]
PANTHERiPTHR23338. PTHR23338. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P62320-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSIGVPIKVL HEAEGHIVTC ETNTGEVYRG KLIEAEDNMN CQMSNITVTY
60 70 80 90 100
RDGRVAQLEQ VYIRGSKIRF LILPDMLKNA PMLKSMKNKN QGSGAGRGKA
110 120
AILKAQVAAR GRGRGMGRGN IFQKRR
Length:126
Mass (Da):13,916
Last modified:July 5, 2004 - v1
Checksum:i59A6E78E860AA3E0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK005341 mRNA. Translation: BAB23963.1.
AK006692 mRNA. Translation: BAB24705.1.
AK019453 mRNA. Translation: BAB31729.1.
AK160321 mRNA. Translation: BAE35738.1.
CCDSiCCDS23926.1.
RefSeqiNP_080371.1. NM_026095.4.
UniGeneiMm.392843.
Mm.45151.

Genome annotation databases

EnsembliENSMUST00000020397; ENSMUSP00000020397; ENSMUSG00000020180.
GeneIDi67332.
KEGGimmu:67332.
UCSCiuc007fqm.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK005341 mRNA. Translation: BAB23963.1.
AK006692 mRNA. Translation: BAB24705.1.
AK019453 mRNA. Translation: BAB31729.1.
AK160321 mRNA. Translation: BAE35738.1.
CCDSiCCDS23926.1.
RefSeqiNP_080371.1. NM_026095.4.
UniGeneiMm.392843.
Mm.45151.

3D structure databases

ProteinModelPortaliP62320.
SMRiP62320. Positions 1-84.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi212112. 2 interactions.
IntActiP62320. 5 interactions.
MINTiMINT-124943.
STRINGi10090.ENSMUSP00000020397.

PTM databases

iPTMnetiP62320.
PhosphoSiteiP62320.
SwissPalmiP62320.

Proteomic databases

EPDiP62320.
MaxQBiP62320.
PaxDbiP62320.
PeptideAtlasiP62320.
PRIDEiP62320.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000020397; ENSMUSP00000020397; ENSMUSG00000020180.
GeneIDi67332.
KEGGimmu:67332.
UCSCiuc007fqm.1. mouse.

Organism-specific databases

CTDi6634.
MGIiMGI:1914582. Snrpd3.

Phylogenomic databases

eggNOGiKOG3172. Eukaryota.
COG1958. LUCA.
GeneTreeiENSGT00610000086153.
HOGENOMiHOG000182712.
HOVERGENiHBG105305.
InParanoidiP62320.
KOiK11088.
OMAiEGHVVTC.
OrthoDBiEOG7VTDQF.
PhylomeDBiP62320.
TreeFamiTF354302.

Enzyme and pathway databases

ReactomeiR-MMU-109688. Cleavage of Growing Transcript in the Termination Region.
R-MMU-111367. SLBP independent Processing of Histone Pre-mRNAs.
R-MMU-191859. snRNP Assembly.
R-MMU-72163. mRNA Splicing - Major Pathway.
R-MMU-72165. mRNA Splicing - Minor Pathway.
R-MMU-77588. SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs.

Miscellaneous databases

PROiP62320.
SOURCEiSearch...

Gene expression databases

BgeeiP62320.
CleanExiMM_SNRPD3.
GenevisibleiP62320. MM.

Family and domain databases

InterProiIPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
[Graphical view]
PANTHERiPTHR23338. PTHR23338. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Cerebellum, Head, Lung and Testis.
  2. "Three proteins of the U7-specific Sm ring function as the molecular ruler to determine the site of 3'-end processing in mammalian histone pre-mRNA."
    Yang X.-C., Torres M.P., Marzluff W.F., Dominski Z.
    Mol. Cell. Biol. 29:4045-4056(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: RNA-BINDING.
  3. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas, Spleen and Testis.

Entry informationi

Entry nameiSMD3_MOUSE
AccessioniPrimary (citable) accession number: P62320
Secondary accession number(s): P43331, Q3TV81
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: July 6, 2016
This is version 102 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.