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P62314 (SMD1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 116. 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 D1

Short name=Sm-D1
Alternative name(s):
Sm-D autoantigen
snRNP core protein D1
Gene names
Name:SNRPD1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length119 AA.
Sequence statusComplete.
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. May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through nonspecific electrostatic contacts with RNA. Ref.12 Ref.18

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. 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.9 Ref.10 Ref.12 Ref.18

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.12

Post-translational modification

Methylated on arginine residues by PRMT5 and PRMT7; probable asymmetric dimethylation which is required for assembly and biogenesis of snRNPs. Ref.8 Ref.11

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
   Molecular functionRibonucleoprotein
   PTMMethylation
   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

mRNA splicing, via spliceosome

Inferred by curator Ref.9. Source: UniProtKB

ncRNA metabolic process

Traceable author statement. Source: Reactome

spliceosomal complex assembly

Traceable author statement PubMed 7527560. Source: ProtInc

spliceosomal snRNP assembly

Inferred from direct assay Ref.12. Source: UniProtKB

   Cellular_componentSMN-Sm protein complex

Inferred from direct assay Ref.12. Source: UniProtKB

U1 snRNP

Inferred from direct assay Ref.16. Source: UniProtKB

U12-type spliceosomal complex

Inferred from direct assay Ref.10. Source: UniProtKB

U4 snRNP

Inferred from direct assay Ref.17. Source: UniProtKB

catalytic step 2 spliceosome

Inferred from direct assay Ref.9. Source: UniProtKB

cytosol

Inferred from direct assay Ref.12. Source: UniProtKB

methylosome

Inferred from direct assay Ref.12. Source: UniProtKB

nucleoplasm

Traceable author statement. Source: Reactome

nucleus

Traceable author statement Ref.1. Source: ProtInc

pICln-Sm protein complex

Inferred from direct assay Ref.12. Source: UniProtKB

small nuclear ribonucleoprotein complex

Traceable author statement PubMed 7527560. Source: ProtInc

   Molecular_functionRNA binding

Traceable author statement Ref.1. Source: ProtInc

poly(A) RNA binding

Inferred from direct assay PubMed 22658674PubMed 22681889. Source: UniProtKB

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

CLNS1AP541056EBI-372177,EBI-724693

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 119119Small nuclear ribonucleoprotein Sm D1
PRO_0000122201

Regions

Region1 – 8080Sufficient for interaction with CLNS1A
Compositional bias86 – 11934Arg/Lys-rich (basic)

Experimental info

Mutagenesis581L → K: Loss of interaction with CLNS1A. Ref.8
Mutagenesis601I → R: Loss of interaction with CLNS1A. Ref.8

Secondary structure

................. 119
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P62314 [UniParc].

Last modified July 5, 2004. Version 1.
Checksum: 0C81C94BF98E0810

FASTA11913,282
        10         20         30         40         50         60 
MKLVRFLMKL SHETVTIELK NGTQVHGTIT GVDVSMNTHL KAVKMTLKNR EPVQLETLSI 

        70         80         90        100        110 
RGNNIRYFIL PDSLPLDTLL VDVEPKVKSK KREAVAGRGR GRGRGRGRGR GRGRGGPRR 

« Hide

References

« Hide 'large scale' references
[1]"Molecular cloning of a cDNA encoding the human Sm-D autoantigen."
Rokeach L.A., Haselby J.A., Hoch S.O.
Proc. Natl. Acad. Sci. U.S.A. 85:4832-4836(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 1-11.
Tissue: Placenta.
[2]Rokeach L.A.
Submitted (JUL-1988) to the EMBL/GenBank/DDBJ databases
Cited for: SEQUENCE REVISION.
[3]"Expression of the major human ribonucleoprotein (RNP) autoantigens in Escherichia coli and their use in an EIA for screening sera from patients with autoimmune diseases."
Renz M., Heim C., Braeunling O., Czichos A., Wieland C., Seelig H.P.
Clin. Chem. 35:1861-1863(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[4]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[5]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].
[6]"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].
[7]"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: Eye.
[8]"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, INTERACTION WITH CLNS1A, MUTAGENESIS OF LEU-58 AND ILE-60.
[9]"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.
[10]"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.
[11]"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.
[12]"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.
[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 (2.5 ANGSTROMS) OF 2-81 IN COMPLEX WITH SNRPD2.
[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]"Functional organization of the Sm core in the crystal structure of human U1 snRNP."
Weber G., Trowitzsch S., Kastner B., Luhrmann R., Wahl M.C.
EMBO J. 29:4172-4184(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.40 ANGSTROMS) IN SPLICEOSOMAL U1 SNRNP.
[17]"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.
[18]"Structural basis of assembly chaperone-mediated snRNP formation."
Grimm C., Chari A., Pelz J.P., Kuper J., Kisker C., Diederichs K., Stark H., Schindelin H., Fischer U.
Mol. Cell 49:692-703(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN 6S PICLN-SM COMPLEX, IDENTIFICATION IN 6S PICLN-SM COMPLEX, FUNCTION IN CORE U1 SNRNP BIOGENESIS.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J03798 mRNA. Translation: AAA36620.1.
L36188 expand/collapse EMBL AC list , L36182, L36186, L36187 Genomic DNA. Translation: AAA85339.1.
CR542239 mRNA. Translation: CAG47035.1.
AB451227 mRNA. Translation: BAG70041.1.
AB451350 mRNA. Translation: BAG70164.1.
CH471088 Genomic DNA. Translation: EAX01130.1.
BC001721 mRNA. Translation: AAH01721.1.
BC072427 mRNA. Translation: AAH72427.1.
PIRA27668. A94201.
RefSeqNP_008869.1. NM_006938.2.
UniGeneHs.464734.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1B34X-ray2.50A1-119[»]
1VU2X-ray3.10A/I/Q/Y/g/o/w1-119[»]
1VU3X-ray3.10A/I/Q/Y/g/o1-119[»]
2Y9AX-ray3.60B/I/P1-119[»]
2Y9BX-ray3.60B/I/P1-119[»]
2Y9CX-ray3.60B/I/P1-119[»]
2Y9DX-ray3.60B/I/P1-119[»]
3CW1X-ray5.49B/M/N/O1-119[»]
3PGWX-ray4.40U/X1-119[»]
3S6NX-ray2.50A1-119[»]
4F77X-ray3.10A/I/Q/Y/g/o/w1-119[»]
4F7UX-ray1.90A/C1-119[»]
ProteinModelPortalP62314.
SMRP62314. Positions 1-96.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid112516. 105 interactions.
DIPDIP-31207N.
IntActP62314. 39 interactions.
MINTMINT-1530147.
STRING9606.ENSP00000300413.

PTM databases

PhosphoSiteP62314.

Polymorphism databases

DMDM51338665.

Proteomic databases

PaxDbP62314.
PeptideAtlasP62314.
PRIDEP62314.

Protocols and materials databases

DNASU6632.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000300413; ENSP00000300413; ENSG00000167088.
GeneID6632.
KEGGhsa:6632.
UCSCuc002ktj.1. human.

Organism-specific databases

CTD6632.
GeneCardsGC18P019192.
HGNCHGNC:11158. SNRPD1.
HPAHPA040516.
MIM601063. gene.
neXtProtNX_P62314.
PharmGKBPA164742464.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG1958.
HOGENOMHOG000182713.
HOVERGENHBG061491.
InParanoidP62314.
KOK11087.
OMAQMNTALR.
OrthoDBEOG7BZVWB.
PhylomeDBP62314.
TreeFamTF314224.

Enzyme and pathway databases

ReactomeREACT_21257. Metabolism of RNA.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpressP62314.
BgeeP62314.
CleanExHS_SNRPD1.
GenevestigatorP62314.

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

ChiTaRSSNRPD1. human.
EvolutionaryTraceP62314.
GeneWikiSmall_nuclear_ribonucleoprotein_D1.
GenomeRNAi6632.
NextBio25835.
PROP62314.
SOURCESearch...

Entry information

Entry nameSMD1_HUMAN
AccessionPrimary (citable) accession number: P62314
Secondary accession number(s): B5BTZ1, P13641
Entry history
Integrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: April 16, 2014
This is version 116 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 18

Human chromosome 18: entries, gene names and cross-references to MIM