Small nuclear ribonucleoprotein Sm D1

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Reviewed, UniProtKB/Swiss-Prot P62314 (SMD1_HUMAN)

Last modified July 7, 2009. Version 66. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Small nuclear ribonucleoprotein Sm D1
      Short name=Sm-D1
Alternative name(s):
    snRNP core protein D1
    Sm-D autoantigen

Gene names

Name:

SNRPD1

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

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Protein attributes

Sequence length	119 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through nonspecific electrostatic contacts with RNA.
Subunit structure	Identified in the spliceosome C complex, at least composed of AQR, ASCC3L1, C19orf29, CDC40, CDC5L, CRNKL1, DDX23, DDX41, DDX48, DDX5, DGCR14, DHX35, DHX38, DHX8, EFTUD2, FRG1, GPATC1, HNRPA1, HNRPA2B1, HNRPA3, HNRPC, HNRPF, HNRPH1, HNRPK, HNRPM, HNRPR, HNRPU, KIAA1160, KIAA1604, LSM2, LSM3, MAGOH, MORG1, PABPC1, PLRG1, PNN, PPIE, PPIL1, PPIL3, PPWD1, PRPF19, PRPF4B, PRPF6, PRPF8, RALY, RBM22, RBM8A, RBMX, SART1, SF3A1, SF3A2, SF3A3, SF3B1, SF3B2, SF3B3, SFRS1, SKIV2L2, SNRPA1, SNRPB, SNRPB2, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, SNW1, SRRM1, SRRM2, SYF2, SYNCRIP, TFIP11, THOC4, U2AF1, WDR57, XAB2 and ZCCHC8.
Subcellular location	Nucleus.
Post-translational modification	Methylated on arginine residues by PRMT5 and PRMT7; methylation is required for assembly and biogenesis of snRNPs.
Involvement in disease	In the autoimmune disease systemic lupus erythematosus, antinuclear antibodies are developed with Sm specificity.
Sequence similarities	Belongs to the snRNP core protein family.

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Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Nucleus Spliceosome
Disease	Systemic lupus erythematosus
Domain	Repeat
Molecular function	Ribonucleoprotein
PTM	Methylation
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	spliceosomal snRNP biogenesis Inferred from Experiment. Source: Reactome spliceosome assembly Traceable author statement. Source: ProtInc
Cellular component	cytosol Inferred from Experiment. Source: Reactome nucleoplasm Inferred from Experiment. Source: Reactome small nuclear ribonucleoprotein complex Traceable author statement. Source: ProtInc spliceosome Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	RNA binding Ref.1 Traceable author statement. Source: ProtInc protein binding Inferred from physical interaction. Source: UniProtKB
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
LSM8	O95777	1	EBI-372177,EBI-347779

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 119

119

Small nuclear ribonucleoprotein Sm D1

PRO_0000122201

Regions

Compositional bias

86 – 119

Arg/Lys-rich (basic)

Secondary structure

119

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P62314-1 [UniParc].

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

119

13,282

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

        70         80         90        100        110 
RGNNIRYFIL PDSLPLDTLL VDVEPKVKSK KREAVAGRGR GRGRGRGRGR GRGRGGPRR

« Hide

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References

	« Hide 'large scale' referencesShow '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: 3260384] [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: 2528429] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[4]	"Cloning of human full-length CDSs in BD Creator(TM) system donor vector." Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A. Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Eye.
[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: 11747828] [Abstract] Cited for: METHYLATION.
[7]	"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: 11991638] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE SPICEOSOMAL C COMPLEX.
[8]	"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: 17709427] [Abstract] Cited for: METHYLATION, INTERACTION WITH PRMT5 AND PRMT7.
[9]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[10]	"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: 10025403] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 2-81 IN COMPLEX WITH SNRPD2.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

J03798 mRNA. Translation: AAA36620.1.
L36188

L36187 Genomic DNA. Translation: AAA85339.1.
CR542239 mRNA. Translation: CAG47035.1.
BC001721 mRNA. Translation: AAH01721.1.
BC072427 mRNA. Translation: AAH72427.1.

IPI

IPI00302850.

PIR

A27668. A94201.

RefSeq

NP_008869.1.

UniGene

Hs.464734

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1B34	X-ray	2.50	A	1-119	[»]
3CW1	X-ray	5.49	B/M/N/O	1-119	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P62314. 12 interactions.

PTM databases

PhosphoSite

P62314.

Proteomic databases

PeptideAtlas

P62314.

PRIDE

P62314.

Genome annotation databases

Ensembl

ENSG00000167088. Homo sapiens. [Contig view]

GeneID

6632.

KEGG

hsa:6632.

UCSC

uc002ktj.1. human.

Organism-specific databases

GeneCards

GC01M044361.
GC18P017446.

H-InvDB

HIX0014358.

HGNC

HGNC:11158. SNRPD1.

MIM

601063. gene.

PharmGKB

PA35999.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

P62314.

HOVERGEN

P62314.

Enzyme and pathway databases

Reactome

REACT_11052. Metabolism of non-coding RNA.
REACT_125. Processing of Capped Intron-Containing Pre-mRNA.
REACT_6167. Influenza Infection.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpress

P62314.

Bgee

P62314.

CleanEx

HS_SNRPD1.

GermOnline

ENSG00000167088. Homo sapiens.

Family and domain databases

InterPro

IPR006649. Euk_arc_LSM_core.
IPR001163. LSM_snRNP_core.
[Graphical view]

Pfam

PF01423. LSM. 1 hit.
[Graphical view]

SMART

SM00651. Sm. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

25835.

SOURCE

Search...

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Entry information

Entry name

SMD1_HUMAN

Accession

Primary (citable) accession number: P62314
Secondary accession number(s): P13641

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 5, 2004
Last sequence update:	July 5, 2004
Last modified:	July 7, 2009
This is version 66 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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Relevant documents

Human chromosome 18

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

MIM cross-references

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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents