P62314 (SMD1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Small nuclear ribonucleoprotein Sm D1
Short name=Sm-D1

Alternative name(s):
Sm-D autoantigen
snRNP core protein D1

Gene names

Name:

SNRPD1

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	119 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

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. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Ref.9 Ref.10
Subcellular location	Nucleus.
Post-translational modification	Methylated on arginine residues by PRMT5 and PRMT7; methylation 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 process	mRNA processing mRNA splicing
Cellular component	Nucleus Spliceosome
Domain	Repeat
Molecular function	Ribonucleoprotein
PTM	Methylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	ncRNA metabolic process Traceable author statement. Source: Reactome spliceosomal complex assembly Traceable author statement PubMed 7527560. Source: ProtInc spliceosomal snRNP assembly Traceable author statement. Source: Reactome
Cellular_component	U12-type spliceosomal complex Inferred from direct assay Ref.10. Source: UniProtKB catalytic step 2 spliceosome Inferred from direct assay Ref.9. Source: UniProtKB cytosol Traceable author statement. Source: Reactome nucleoplasm Traceable author statement. Source: Reactome small nuclear ribonucleoprotein complex Traceable author statement PubMed 7527560. Source: ProtInc
Molecular_function	RNA binding Traceable author statement Ref.1. Source: ProtInc
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CLNS1A	P54105	5	EBI-372177,EBI-724693

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

34

Arg/Lys-rich (basic)

Secondary structure

1

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.

.

119

Helix Strand Turn

Details...

Helix

3 – 8

6

Beta strand

14 – 19

6

Beta strand

24 – 32

9

Beta strand

38 – 46

9

Beta strand

53 – 60

8

Helix

62 – 64

3

Beta strand

65 – 69

5

Helix

76 – 79

4

Sequences

	Sequence		Length	Mass (Da)
	P62314 [UniParc]. Last modified July 5, 2004. Version 1. Checksum: 0C81C94BF98E0810	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

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] [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. , 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. , 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.
[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, 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]	"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].
[13]	"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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J03798 mRNA. Translation: AAA36620.1.
L36188 , 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.

IPI

IPI00302850.

PIR

A27668. A94201.

RefSeq

NP_008869.1. NM_006938.2.

UniGene

Hs.464734.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1B34	X-ray	2.50	A	1-119	[»]
1VU2	X-ray	3.10	A/I/Q/Y/g/o/w	1-119	[»]
1VU3	X-ray	3.10	A/I/Q/Y/g/o	1-119	[»]
2Y9A	X-ray	3.60	B/I/P	1-119	[»]
2Y9B	X-ray	3.60	B/I/P	1-119	[»]
2Y9C	X-ray	3.60	B/I/P	1-119	[»]
2Y9D	X-ray	3.60	B/I/P	1-119	[»]
3CW1	X-ray	5.49	B/M/N/O	1-119	[»]
3PGW	X-ray	4.40	U/X	1-119	[»]
3S6N	X-ray	2.50	A	1-119	[»]
4F77	X-ray	3.10	A/I/Q/Y/g/o/w	1-119	[»]

ProteinModelPortal

P62314.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-31207N.

IntAct

P62314. 31 interactions.

MINT

MINT-1530147.

STRING

9606.ENSP00000300413.

PTM databases

PhosphoSite

P62314.

Polymorphism databases

DMDM

51338665.

Proteomic databases

PaxDb

P62314.

PeptideAtlas

P62314.

PRIDE

P62314.

Protocols and materials databases

DNASU

6632.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000300413; ENSP00000300413; ENSG00000167088.

GeneID

6632.

KEGG

hsa:6632.

UCSC

uc002ktj.1. human.

Organism-specific databases

CTD

6632.

GeneCards

GC18P019192.

HGNC

HGNC:11158. SNRPD1.

HPA

HPA040516.

MIM

601063. gene.

neXtProt

NX_P62314.

PharmGKB

PA164742464.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG1958.

HOGENOM

HOG000182713.

HOVERGEN

HBG061491.

InParanoid

P62314.

KO

K11087.

OMA

KMTIKNR.

OrthoDB

EOG4933KF.

PhylomeDB

P62314.

Enzyme and pathway databases

Reactome

REACT_1675. mRNA Processing.
REACT_21257. Metabolism of RNA.
REACT_71. Gene Expression.

Gene expression databases

Bgee

P62314.

CleanEx

HS_SNRPD1.

Genevestigator

P62314.

GermOnline

ENSG00000167088. Homo sapiens.

Family and domain databases

InterPro

IPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view]

PANTHER

PTHR23338. PTHR23338. 1 hit.

Pfam

PF01423. LSM. 1 hit.
[Graphical view]

SMART

SM00651. Sm. 1 hit.
[Graphical view]

SUPFAM

SSF50182. Sm_like_riboprot. 1 hit.

ProtoNet

Search...

Other

ChiTaRS

SNRPD1. human.

EvolutionaryTrace

P62314.

GenomeRNAi

6632.

NextBio

25835.

SOURCE

Search...

Entry information

Entry name

SMD1_HUMAN

Accession

Primary (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:	May 1, 2013
This is version 106 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.