P62316 (SMD2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

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) [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	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. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Ref.7 Ref.8
Subcellular location	Nucleus.
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
Coding sequence diversity	Alternative splicing
Molecular function	Ribonucleoprotein
PTM	Acetylation Phosphoprotein
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 Ref.1. Source: ProtInc spliceosomal snRNP assembly Traceable author statement. Source: Reactome
Cellular_component	U12-type spliceosomal complex Inferred from direct assay Ref.8. Source: UniProtKB catalytic step 2 spliceosome Inferred from direct assay Ref.7. Source: UniProtKB cytosol Traceable author statement. Source: Reactome nucleoplasm Traceable author statement. Source: Reactome small nuclear ribonucleoprotein complex Traceable author statement PubMed 1701240. Source: ProtInc
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: P62316-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: P62316-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-10: Missing.

Note: No experimental confirmation available.

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

Modified residue

12

1

Phosphothreonine Ref.10

Natural variations

Alternative sequence

1 – 10

10

Missing in isoform 2.

VSP_045371

Experimental info

Sequence conflict

38

1

N → S in BU531743. Ref.5

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

118

Helix Strand Turn

Details...

Beta strand

25 – 27

3

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)
	Isoform 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
	Isoform 2 [UniParc]. Checksum: 3E92B3D47F961A7F	FASTA	108	12,399
	10 20 30 40 50 60 MTPEELQKRE EEEFNTGPLS VLTQSVKNNT QVLINCRNNK KLLGRVKAFD RHCNMVLENV 70 80 90 100 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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), 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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2). 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] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE SPLICEOSOMAL C COMPLEX.
[8]	"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.
[9]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Cervix carcinoma.
[10]	"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis." Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M. Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-12, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[11]	"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].
[12]	"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 26-118 IN COMPLEX WITH SNRPD1.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U15008 mRNA. Translation: AAC13776.1.
AK291912 mRNA. Translation: BAF84601.1.
AC007191 Genomic DNA. Translation: AAD22673.1.
CH471126 Genomic DNA. Translation: EAW57373.1.
CH471126 Genomic DNA. Translation: EAW57374.1.
BC000486 mRNA. Translation: AAH00486.1.
BC001930 mRNA. Translation: AAH01930.1.
BU531743 mRNA. No translation available.

IPI

IPI00017963.

PIR

I38861.

RefSeq

NP_004588.1. NM_004597.5.
NP_808210.2. NM_177542.2.

UniGene

Hs.515472.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1B34	X-ray	2.50	B	1-118	[»]
1VU2	X-ray	3.10	B/J/R/Z/h/p/x	1-118	[»]
1VU3	X-ray	3.10	B/J/R/Z/h/p	1-118	[»]
2Y9A	X-ray	3.60	C/J/Q	1-118	[»]
2Y9B	X-ray	3.60	C/J/Q	1-118	[»]
2Y9C	X-ray	3.60	C/J/Q	1-118	[»]
2Y9D	X-ray	3.60	C/J/Q	1-118	[»]
3CW1	X-ray	5.49	C/P/Q/R	1-118	[»]
3PGW	X-ray	4.40	V/Y	1-118	[»]
3S6N	X-ray	2.50	B	1-118	[»]
4F77	X-ray	3.10	B/J/R/Z/h/p/x	1-118	[»]

ProteinModelPortal

P62316.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-31219N.

IntAct

P62316. 27 interactions.

MINT

MINT-5002672.

STRING

9606.ENSP00000342374.

PTM databases

PhosphoSite

P62316.

Polymorphism databases

DMDM

51338666.

Proteomic databases

PaxDb

P62316.

PeptideAtlas

P62316.

PRIDE

P62316.

Protocols and materials databases

DNASU

6633.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000342669; ENSP00000342374; ENSG00000125743.
ENST00000391932; ENSP00000375798; ENSG00000125743.
ENST00000587367; ENSP00000465952; ENSG00000125743.
ENST00000588301; ENSP00000465216; ENSG00000125743.
ENST00000588599; ENSP00000466152; ENSG00000125743.

GeneID

6633.

KEGG

hsa:6633.

UCSC

uc002pcv.3. human.

Organism-specific databases

CTD

6633.

GeneCards

GC19M046190.

HGNC

HGNC:11159. SNRPD2.

HPA

HPA041437.

MIM

601061. gene.

neXtProt

NX_P62316.

PharmGKB

PA36000.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG1958.

HOGENOM

HOG000223545.

HOVERGEN

HBG054415.

InParanoid

P62316.

KO

K11096.

OMA

VKELWTE.

OrthoDB

EOG4PC9TN.

PhylomeDB

P62316.

Enzyme and pathway databases

Reactome

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

Gene expression databases

Bgee

P62316.

CleanEx

HS_SNRPD1.
HS_SNRPD2.

Genevestigator

P62316.

GermOnline

ENSG00000125743. Homo sapiens.

Family and domain databases

InterPro

IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
IPR027248. Sm_D2.
[Graphical view]

PANTHER

PTHR12777. PTHR12777. 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

EvolutionaryTrace

P62316.

GenomeRNAi

6633.

NextBio

25839.

SOURCE

Search...

Entry information

Entry name

SMD2_HUMAN

Accession

Primary (citable) accession number: P62316
Secondary accession number(s): A8K797, J3KPM5, P43330

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 5, 2004
Last sequence update:	July 5, 2004
Last modified:	May 1, 2013
This is version 104 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.