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P62318 (SMD3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 112. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Small nuclear ribonucleoprotein Sm D3

Short name=Sm-D3
Alternative name(s):
snRNP core protein D3
Gene names
Name:SNRPD3
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length126 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 an 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. Ref.7 Ref.11

Subunit structure

U1 snRNP is for instance composed of the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in an 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. Ref.7 Ref.8 Ref.9 Ref.11

Subcellular location

Cytoplasmcytosol. Nucleus. Note: SMN-mediated assembly into core snRNPs occurs in the cytosol before SMN-mediated transport to the nucleus to be included in spliceosomes. Ref.11

Post-translational modification

Methylated on arginine residues by PRMT5 and PRMT7; probable asymmetric dimethylation which is required for assembly and biogenesis of snRNPs. Ref.6 Ref.10

Miscellaneous

In the autoimmune disease systemic lupus erythematosus, antinuclear antibodies are developed with Sm specificity.

Sequence similarities

Belongs to the snRNP core protein family.

Ontologies

Keywords
   Biological processmRNA processing
mRNA splicing
   Cellular componentCytoplasm
Nucleus
Spliceosome
   DomainRepeat
   LigandRNA-binding
   Molecular functionRibonucleoprotein
   PTMAcetylation
Methylation
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processRNA metabolic process

Traceable author statement. Source: Reactome

RNA splicing

Traceable author statement. Source: Reactome

gene expression

Traceable author statement. Source: Reactome

histone mRNA metabolic process

Traceable author statement. Source: Reactome

mRNA 3'-end processing

Traceable author statement. Source: Reactome

mRNA splicing, via spliceosome

Inferred by curator Ref.8. Source: UniProtKB

ncRNA metabolic process

Traceable author statement. Source: Reactome

spliceosomal snRNP assembly

Inferred from direct assay Ref.11. Source: UniProtKB

termination of RNA polymerase II transcription

Traceable author statement. Source: Reactome

transcription from RNA polymerase II promoter

Traceable author statement. Source: Reactome

   Cellular_componentSMN-Sm protein complex

Inferred from direct assay Ref.11. Source: UniProtKB

U1 snRNP

Inferred from direct assay PubMed 21113136. Source: UniProtKB

U12-type spliceosomal complex

Inferred from direct assay Ref.9. Source: UniProtKB

U4 snRNP

Inferred from direct assay Ref.16. Source: UniProtKB

U7 snRNP

Inferred from direct assay Ref.7. Source: UniProtKB

catalytic step 2 spliceosome

Inferred from direct assay Ref.8. Source: UniProtKB

cytoplasm

Inferred from direct assay. Source: HPA

cytosol

Inferred from direct assay Ref.11. Source: UniProtKB

methylosome

Inferred from direct assay Ref.11. Source: UniProtKB

nucleoplasm

Traceable author statement. Source: Reactome

nucleus

Inferred from direct assay. Source: HPA

pICln-Sm protein complex

Inferred from direct assay Ref.11. Source: UniProtKB

small nuclear ribonucleoprotein complex

Traceable author statement PubMed 1701240. Source: ProtInc

spliceosomal complex

Traceable author statement Ref.1. Source: ProtInc

   Molecular_functionenzyme binding

Inferred from physical interaction Ref.10. Source: UniProtKB

histone pre-mRNA DCP binding

Inferred from sequence or structural similarity. Source: UniProtKB

poly(A) RNA binding

Inferred from direct assay PubMed 22681889. Source: UniProtKB

protein binding

Inferred from physical interaction PubMed 11714716PubMed 11748230PubMed 12065586. Source: UniProtKB

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.12
Chain2 – 126125Small nuclear ribonucleoprotein Sm D3
PRO_0000122214

Regions

Repeat110 – 11121
Repeat112 – 11322
Repeat114 – 11523
Repeat116 – 11724
Repeat118 – 11925
Region110 – 119105 X 2 AA tandem repeats of [RM]-G
Compositional bias84 – 12643Arg/Lys-rich (basic)

Amino acid modifications

Modified residue21N-acetylserine Ref.12

Secondary structure

.............. 126
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P62318 [UniParc].

Last modified July 5, 2004. Version 1.
Checksum: 59A6E78E860AA3E0

FASTA12613,916
        10         20         30         40         50         60 
MSIGVPIKVL HEAEGHIVTC ETNTGEVYRG KLIEAEDNMN CQMSNITVTY RDGRVAQLEQ 

        70         80         90        100        110        120 
VYIRGSKIRF LILPDMLKNA PMLKSMKNKN QGSGAGRGKA AILKAQVAAR GRGRGMGRGN 


IFQKRR 

« Hide

References

« Hide 'large scale' references
[1]"cDNA cloning of the Sm proteins D2 and D3 from human small nuclear ribonucleoproteins: evidence for a direct D1-D2 interaction."
Lehmeier T., Raker V., Hermann H., Luehrmann R.
Proc. Natl. Acad. Sci. U.S.A. 91:12317-12321(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE.
[2]"A genome annotation-driven approach to cloning the human ORFeome."
Collins J.E., Wright C.L., Edwards C.A., Davis M.P., Grinham J.A., Cole C.G., Goward M.E., Aguado B., Mallya M., Mokrab Y., Huckle E.J., Beare D.M., Dunham I.
Genome Biol. 5:R84.1-R84.11(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[3]"Human protein factory for converting the transcriptome into an in vitro-expressed proteome."
Goshima N., Kawamura Y., Fukumoto A., Miura A., Honma R., Satoh R., Wakamatsu A., Yamamoto J., Kimura K., Nishikawa T., Andoh T., Iida Y., Ishikawa K., Ito E., Kagawa N., Kaminaga C., Kanehori K., Kawakami B. expand/collapse author list , Kenmochi K., Kimura R., Kobayashi M., Kuroita T., Kuwayama H., Maruyama Y., Matsuo K., Minami K., Mitsubori M., Mori M., Morishita R., Murase A., Nishikawa A., Nishikawa S., Okamoto T., Sakagami N., Sakamoto Y., Sasaki Y., Seki T., Sono S., Sugiyama A., Sumiya T., Takayama T., Takayama Y., Takeda H., Togashi T., Yahata K., Yamada H., Yanagisawa Y., Endo Y., Imamoto F., Kisu Y., Tanaka S., Isogai T., Imai J., Watanabe S., Nomura N.
Nat. Methods 5:1011-1017(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Lung.
[6]"Methylation of Sm proteins by a complex containing PRMT5 and the putative U snRNP assembly factor pICln."
Meister G., Eggert C., Buehler D., Brahms H., Kambach C., Fischer U.
Curr. Biol. 11:1990-1994(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: METHYLATION.
[7]"Purified U7 snRNPs lack the Sm proteins D1 and D2 but contain Lsm10, a new 14 kDa Sm D1-like protein."
Pillai R.S., Will C.L., Luehrmann R., Schuemperli D., Mueller B.
EMBO J. 20:5470-5479(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, IDENTIFICATION IN THE U7 SNRNP COMPLEX.
[8]"Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis."
Jurica M.S., Licklider L.J., Gygi S.P., Grigorieff N., Moore M.J.
RNA 8:426-439(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE SPLICEOSOMAL C COMPLEX.
[9]"The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome."
Will C.L., Schneider C., Hossbach M., Urlaub H., Rauhut R., Elbashir S., Tuschl T., Luehrmann R.
RNA 10:929-941(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN A COMPLEX WITH THE U11/U12 SPLICEOSOME, IDENTIFICATION BY MASS SPECTROMETRY.
[10]"Two distinct arginine methyltransferases are required for biogenesis of Sm-class ribonucleoproteins."
Gonsalvez G.B., Tian L., Ospina J.K., Boisvert F.-M., Lamond A.I., Matera A.G.
J. Cell Biol. 178:733-740(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: METHYLATION, INTERACTION WITH PRMT5 AND PRMT7.
[11]"An assembly chaperone collaborates with the SMN complex to generate spliceosomal SnRNPs."
Chari A., Golas M.M., Klingenhager M., Neuenkirchen N., Sander B., Englbrecht C., Sickmann A., Stark H., Fischer U.
Cell 135:497-509(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN SNRNP BIOGENESIS, IDENTIFICATION IN 6S PICLN-SM COMPLEX, IDENTIFICATION IN SMN-SM COMPLEX, SUBCELLULAR LOCATION.
[12]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
[13]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[14]"Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs."
Kambach C., Walke S., Young R., Avis J.M., de la Fortelle E., Raker V.A., Luehrmann R., Li J., Nagai K.
Cell 96:375-387(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 4-75 IN COMPLEX WITH SNRPB.
[15]"Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution."
Pomeranz Krummel D.A., Oubridge C., Leung A.K., Li J., Nagai K.
Nature 458:475-480(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (5.49 ANGSTROMS) IN SPLICEOSOMAL U1 SNRNP.
[16]"Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis."
Leung A.K., Nagai K., Li J.
Nature 473:536-539(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.60 ANGSTROMS) IN SPLICEOSOMAL CORE U4 SNRNP.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U15009 mRNA. Translation: AAA57034.1.
CR456583 mRNA. Translation: CAG30469.1.
AB451249 mRNA. Translation: BAG70063.1.
AB451373 mRNA. Translation: BAG70187.1.
CH471095 Genomic DNA. Translation: EAW59670.1.
BC000457 mRNA. Translation: AAH00457.1.
BC003150 mRNA. Translation: AAH03150.1.
CCDSCCDS13828.1.
RefSeqNP_001265585.1. NM_001278656.1.
NP_004166.1. NM_004175.4.
UniGeneHs.356549.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1D3BX-ray2.00A/C/E/G/I/K1-75[»]
2Y9AX-ray3.60D/K/R1-126[»]
2Y9BX-ray3.60D/K/R1-126[»]
2Y9CX-ray3.60D/K/R1-126[»]
2Y9DX-ray3.60D/K/R1-126[»]
3CW1X-ray5.49D/S/T/U1-126[»]
3PGWX-ray4.40W/Z1-126[»]
3VRIX-ray1.60C54-63[»]
ProteinModelPortalP62318.
SMRP62318. Positions 4-92.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid112518. 89 interactions.
DIPDIP-31216N.
IntActP62318. 38 interactions.
MINTMINT-5002679.
STRING9606.ENSP00000215829.

PTM databases

PhosphoSiteP62318.

Polymorphism databases

DMDM51338667.

Proteomic databases

MaxQBP62318.
PaxDbP62318.
PeptideAtlasP62318.
PRIDEP62318.

Protocols and materials databases

DNASU6634.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000215829; ENSP00000215829; ENSG00000100028.
ENST00000404603; ENSP00000456090; ENSG00000100028.
GeneID6634.
KEGGhsa:6634.
UCSCuc003aam.1. human.

Organism-specific databases

CTD6634.
GeneCardsGC22P024951.
HGNCHGNC:11160. SNRPD3.
HPAHPA001170.
MIM601062. gene.
neXtProtNX_P62318.
PharmGKBPA36001.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG1958.
HOGENOMHOG000182712.
HOVERGENHBG105305.
InParanoidP62318.
KOK11088.
OMAIMRANAR.
OrthoDBEOG7VTDQF.
PhylomeDBP62318.
TreeFamTF354302.

Enzyme and pathway databases

ReactomeREACT_1788. Transcription.
REACT_21257. Metabolism of RNA.
REACT_71. Gene Expression.
REACT_78. Post-Elongation Processing of the Transcript.

Gene expression databases

ArrayExpressP62318.
BgeeP62318.
CleanExHS_SNRPD3.
GenevestigatorP62318.

Family and domain databases

InterProIPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view]
PANTHERPTHR23338. PTHR23338. 1 hit.
PfamPF01423. LSM. 1 hit.
[Graphical view]
SMARTSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMSSF50182. SSF50182. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP62318.
GeneWikiSNRPD3.
GenomeRNAi6634.
NextBio25845.
PROP62318.
SOURCESearch...

Entry information

Entry nameSMD3_HUMAN
AccessionPrimary (citable) accession number: P62318
Secondary accession number(s): B5BU13, P43331
Entry history
Integrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: July 9, 2014
This is version 112 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 22

Human chromosome 22: entries, gene names and cross-references to MIM