P62318 (SMD3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Small nuclear ribonucleoprotein Sm D3
Short name=Sm-D3

Alternative name(s):
snRNP core protein D3

Gene names

Name:

SNRPD3

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	126 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Appears to function in the U7 snRNP complex that is involved in histone 3'-end processing. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner. Ref.7
Subunit structure	Component of the heptameric ring U7 snRNP complex, or U7 Sm protein core complex, at least composed of LSM10, LSM11, SNRPB, SNRPD3, SNRPE, SNRPF, SNRPG and U7 snRNA. Formation of the U7 snRNP is an ATP-dependent process mediated by a specialized SMN complex containing at least the Sm protein core complex and additionally, the U7-specific LSM10 and LSM11 proteins. Identified in the spliceosome C complex. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Ref.7 Ref.8 Ref.9
Subcellular location	Nucleus.
Post-translational modification	Methylated on arginine residues by PRMT5 and PRMT7; methylation is required for assembly and biogenesis of snRNPs. Ref.6 Ref.10 Arg-97 is dimethylated, probably to asymmetric dimethylarginine. Ref.6 Ref.10
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
Ligand	RNA-binding
Molecular function	Ribonucleoprotein
PTM	Methylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	histone mRNA metabolic process Traceable author statement. Source: Reactome ncRNA metabolic process Traceable author statement. Source: Reactome spliceosomal snRNP assembly Traceable author statement. Source: Reactome termination of RNA polymerase II transcription Traceable author statement. Source: Reactome
Cellular_component	U12-type spliceosomal complex Inferred from direct assay Ref.9. Source: UniProtKB U7 snRNP Inferred from direct assay Ref.7. Source: UniProtKB catalytic step 2 spliceosome Inferred from direct assay Ref.8. Source: UniProtKB cytosol Traceable author statement. Source: Reactome nucleoplasm Traceable author statement. Source: Reactome
Molecular_function	histone pre-mRNA DCP binding Inferred from sequence or structural similarity. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CLNS1A	P54105	5	EBI-372789,EBI-724693

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 126

126

Small nuclear ribonucleoprotein Sm D3

PRO_0000122214

Regions

Repeat

110 – 111

2

1

Repeat

112 – 113

2

2

Repeat

114 – 115

2

3

Repeat

116 – 117

2

4

Repeat

118 – 119

2

5

Region

110 – 119

10

5 X 2 AA tandem repeats of [RM]-G

Compositional bias

84 – 126

43

Arg/Lys-rich (basic)

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

126

Helix Strand Turn

Details...

Helix

6 – 12

7

Turn

13 – 15

3

Beta strand

16 – 22

7

Beta strand

27 – 35

9

Beta strand

41 – 49

9

Beta strand

55 – 63

9

Helix

65 – 67

3

Beta strand

68 – 73

6

Sequences

	Sequence		Length	Mass (Da)
	P62318 [UniParc]. Last modified July 5, 2004. Version 1. Checksum: 59A6E78E860AA3E0	FASTA	126	13,916
	10 20 30 40 50 60 MSIGVPIKVL HEAEGHIVTC ETNTGEVYRG KLIEAEDNMN CQMSNITVTY RDGRVAQLEQ 70 80 90 100 110 120 VYIRGSKIRF LILPDMLKNA PMLKSMKNKN QGSGAGRGKA AILKAQVAAR GRGRGMGRGN IFQKRR

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], PARTIAL PROTEIN SEQUENCE.
[2]	"A genome annotation-driven approach to cloning the human ORFeome." Collins J.E., Wright C.L., Edwards C.A., Davis M.P., Grinham J.A., Cole C.G., Goward M.E., Aguado B., Mallya M., Mokrab Y., Huckle E.J., Beare D.M., Dunham I. Genome Biol. 5:R84.1-R84.11(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[3]	"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].
[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]. Tissue: Lung.
[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] [Europe PMC] [Abstract] Cited for: METHYLATION.
[7]	"Purified U7 snRNPs lack the Sm proteins D1 and D2 but contain Lsm10, a new 14 kDa Sm D1-like protein." Pillai R.S., Will C.L., Luehrmann R., Schuemperli D., Mueller B. EMBO J. 20:5470-5479(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN THE U7 SNRNP COMPLEX.
[8]	"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.
[9]	"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.
[10]	"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.
[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 (2.0 ANGSTROMS) OF 4-75 IN COMPLEX WITH SNRPB.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U15009 mRNA. Translation: AAA57034.1.
CR456583 mRNA. Translation: CAG30469.1.
AB451249 mRNA. Translation: BAG70063.1.
AB451373 mRNA. Translation: BAG70187.1.
CH471095 Genomic DNA. Translation: EAW59670.1.
BC000457 mRNA. Translation: AAH00457.1.
BC003150 mRNA. Translation: AAH03150.1.

IPI

IPI00017964.

RefSeq

NP_004166.1. NM_004175.3.

UniGene

Hs.356549.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1D3B	X-ray	2.00	A/C/E/G/I/K	1-75	[»]
2Y9A	X-ray	3.60	D/K/R	1-126	[»]
2Y9B	X-ray	3.60	D/K/R	1-126	[»]
2Y9C	X-ray	3.60	D/K/R	1-126	[»]
2Y9D	X-ray	3.60	D/K/R	1-126	[»]
3CW1	X-ray	5.49	D/S/T/U	1-126	[»]
3PGW	X-ray	4.40	W/Z	1-126	[»]
3VRI	X-ray	1.60	C	54-63	[»]

ProteinModelPortal

P62318.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-31216N.

IntAct

P62318. 32 interactions.

MINT

MINT-5002679.

STRING

9606.ENSP00000215829.

PTM databases

PhosphoSite

P62318.

Polymorphism databases

DMDM

51338667.

Proteomic databases

PaxDb

P62318.

PeptideAtlas

P62318.

PRIDE

P62318.

Protocols and materials databases

DNASU

6634.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000215829; ENSP00000215829; ENSG00000100028.
ENST00000404603; ENSP00000456090; ENSG00000100028.

GeneID

6634.

KEGG

hsa:6634.

UCSC

uc003aam.1. human.

Organism-specific databases

CTD

6634.

GeneCards

GC22P024951.

HGNC

HGNC:11160. SNRPD3.

HPA

HPA001170.

MIM

601062. gene.

neXtProt

NX_P62318.

PharmGKB

PA36001.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG1958.

HOGENOM

HOG000182712.

HOVERGEN

HBG105305.

InParanoid

P62318.

KO

K11088.

OMA

RNAPMFR.

OrthoDB

EOG4CRM1J.

PhylomeDB

P62318.

Enzyme and pathway databases

Reactome

REACT_1675. mRNA Processing.
REACT_1788. Transcription.
REACT_21257. Metabolism of RNA.
REACT_71. Gene Expression.
REACT_78. Post-Elongation Processing of the Transcript.

Gene expression databases

ArrayExpress

P62318.

Bgee

P62318.

CleanEx

HS_SNRPD3.

Genevestigator

P62318.

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

EvolutionaryTrace

P62318.

GenomeRNAi

6634.

NextBio

25845.

SOURCE

Search...

Entry information

Entry name

SMD3_HUMAN

Accession

Primary (citable) accession number: P62318
Secondary accession number(s): B5BU13, P43331

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 5, 2004
Last sequence update:	July 5, 2004
Last modified:	May 1, 2013
This is version 101 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.