Reviewed, UniProtKB/Swiss-Prot P62316 (SMD2_HUMAN)

Names and origin

Protein names

Recommended name:
    Small nuclear ribonucleoprotein Sm D2
      Short name=Sm-D2
Alternative name(s):
    snRNP core protein D2

Gene names

Name:	SNRPD2
Synonyms:	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

Protein attributes

Sequence length	118 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Required for pre-mRNA splicing. Required for snRNP biogenesis By similarity.
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.
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.

Ontologies

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

Binary interactions

With	Entry	#Exp.	IntAct	Notes
LSM2	Q9Y333	2	EBI-297993,EBI-347416
LSM6	P62312	1	EBI-297993,EBI-373310

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.6

Chain

2 – 118

117

Small nuclear ribonucleoprotein Sm D2

PRO_0000122207

Amino acid modifications

Modified residue

2

1

N-acetylserine Ref.6

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

118

Helix Strand Turn

Details...

Helix

28 – 38

11

Beta strand

41 – 46

6

Beta strand

51 – 59

9

Beta strand

65 – 73

9

Beta strand

94 – 101

8

Helix

103 – 105

3

Beta strand

106 – 111

6

Sequences

	Sequence		Length	Mass (Da)
	P62316-1 [UniParc]. Last modified July 5, 2004. Version 1. Checksum: D986059D82B7E045	FASTA	118	13,527
	10 20 30 40 50 60 MSLLNKPKSE MTPEELQKRE EEEFNTGPLS VLTQSVKNNT QVLINCRNNK KLLGRVKAFD 70 80 90 100 110 RHCNMVLENV KEMWTEVPKS GKGKKKSKPV NKDRYISKMF LRGDSVIVVL RNPLIAGK

References

	« Hide 'large scale' referencesShow '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: 7527560] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 75-96 AND 103-118.
[2]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[3]	"The DNA sequence and biology of human chromosome 19." Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V. , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M. Nature 428:529-535(2004) [PubMed: 15057824] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[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. , 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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Lung.
[6]	Bienvenut W.V., Calvo F., Matallanas D., Cooper W.N., Kolch W. Submitted (FEB-2008) to UniProtKB Cited for: PROTEIN SEQUENCE OF 2-47; 72-79 AND 103-118, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT SER-2, MASS SPECTROMETRY. Tissue: Cervix carcinoma and Mammary carcinoma.
[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]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[9]	"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 26-118 IN COMPLEX WITH SNRPD1.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

U15008 mRNA. Translation: AAC13776.1.
AK291912 mRNA. Translation: BAF84601.1.
AC007191 Genomic DNA. Translation: AAD22673.1.
CH471126 Genomic DNA. Translation: EAW57373.1.
BC000486 mRNA. Translation: AAH00486.1.
BC001930 mRNA. Translation: AAH01930.1.

IPI

IPI00017963.

PIR

I38861.

RefSeq

NP_004588.1.
NP_808210.2.

UniGene

Hs.515472

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1B34	X-ray	2.50	B	1-118	[»]
3CW1	X-ray	5.49	C/P/Q/R	1-118	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P62316. 12 interactions.

STRING

P62316.

PTM databases

PhosphoSite

P62316.

Proteomic databases

PeptideAtlas

P62316.

PRIDE

P62316.

Genome annotation databases

Ensembl

ENST00000342669; ENSP00000342374; ENSG00000125743; Homo sapiens. [Genome view]
ENST00000391932; ENSP00000375798; ENSG00000125743; Homo sapiens. [Genome view]

GeneID

6633.

KEGG

hsa:6633.

UCSC

uc002pcv.1. human.

Organism-specific databases

CTD

6633.

GeneCards

GC10P091728.
GC19M050882.

H-InvDB

HIX0015238.
HIX0035731.

HGNC

HGNC:11159. SNRPD2.

MIM

601061. gene.

PharmGKB

PA36000.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

P62316.

HOVERGEN

P62316.

OMA

EMWTETP.

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

P62316.

Bgee

P62316.

CleanEx

HS_SNRPD1.
HS_SNRPD2.

Genevestigator

P62316.

GermOnline

ENSG00000125743. Homo sapiens.

Family and domain databases

InterPro

IPR006649. Like-Sm_rNuclprot_core_euk/arc.
IPR001163. LSM_snRNP_core.
[Graphical view]

Pfam

PF01423. LSM. 1 hit.
[Graphical view]

ProDom

PD020287. snRNP. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00651. Sm. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

25839.

SOURCE

Search...

Entry information

Entry name

SMD2_HUMAN

Accession

Primary (citable) accession number: P62316
Secondary accession number(s): A8K797, P43330

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 5, 2004
Last sequence update:	July 5, 2004
Last modified:	November 3, 2009
This is version 67 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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.