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Protein

Small nuclear ribonucleoprotein Sm D2

Gene

SNRPD2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP.2 Publications

Miscellaneous

In the autoimmune disease systemic lupus erythematosus, antinuclear antibodies are developed with Sm specificity.

GO - Molecular functioni

  • RNA binding Source: UniProtKB

GO - Biological processi

  • mRNA splicing, via spliceosome Source: Reactome
  • nuclear import Source: Reactome
  • RNA splicing Source: ProtInc
  • spliceosomal complex assembly Source: ProtInc
  • spliceosomal snRNP assembly Source: UniProtKB

Keywordsi

Molecular functionRibonucleoprotein
Biological processmRNA processing, mRNA splicing

Enzyme and pathway databases

ReactomeiR-HSA-191859. snRNP Assembly.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Small nuclear ribonucleoprotein Sm D2
Short name:
Sm-D2
Alternative name(s):
snRNP core protein D2
Gene namesi
Name:SNRPD2
Synonyms:SNRPD1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

EuPathDBiHostDB:ENSG00000125743.10.
HGNCiHGNC:11159. SNRPD2.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000125743.
PharmGKBiPA36000.

Polymorphism and mutation databases

BioMutaiSNRPD2.
DMDMi51338666.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources1 Publication
ChainiPRO_00001222072 – 118Small nuclear ribonucleoprotein Sm D2Add BLAST117

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1 Publication1
Cross-linki6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki8Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei9PhosphoserineCombined sources1
Modified residuei12PhosphothreonineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiP62316.
MaxQBiP62316.
PaxDbiP62316.
PeptideAtlasiP62316.
PRIDEiP62316.
TopDownProteomicsiP62316-1. [P62316-1]
P62316-2. [P62316-2]

PTM databases

iPTMnetiP62316.
PhosphoSitePlusiP62316.
SwissPalmiP62316.

Expressioni

Gene expression databases

BgeeiENSG00000125743.
CleanExiHS_SNRPD1.
HS_SNRPD2.
ExpressionAtlasiP62316. baseline and differential.
GenevisibleiP62316. HS.

Organism-specific databases

HPAiHPA041437.

Interactioni

Subunit structurei

U1 snRNP is for instance composed of the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP, and at least three U1 snRNP-specific proteins SNRNP70/U1-70K, SNRPA/U1-A and SNRPC/U1-C. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Part of the SMN-Sm complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8, STRAP/UNRIP and the Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG; catalyzes core snRNPs assembly. Forms a 6S pICln-Sm complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP.5 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi112517. 127 interactors.
CORUMiP62316.
DIPiDIP-31219N.
IntActiP62316. 45 interactors.
MINTiMINT-5002672.
STRINGi9606.ENSP00000342374.

Structurei

Secondary structure

1118
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi25 – 27Combined sources3
Helixi28 – 38Combined sources11
Beta strandi41 – 46Combined sources6
Beta strandi51 – 59Combined sources9
Beta strandi65 – 73Combined sources9
Beta strandi94 – 101Combined sources8
Helixi103 – 105Combined sources3
Beta strandi106 – 111Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1B34X-ray2.50B1-118[»]
3CW1X-ray5.49C/P/Q/R1-118[»]
3JCRelectron microscopy7.00Q/q1-118[»]
3PGWX-ray4.40V/Y1-118[»]
3S6NX-ray2.50B1-118[»]
4F7UX-ray1.90B/D1-118[»]
4PJOX-ray3.30D/R/d/r1-118[»]
4V98X-ray3.10AB/AJ/AR/AZ/Ah/Ap/Ax/BB/BJ/BR/BZ/Bh/Bp/Bx/CB/CJ/CR/CZ/Ch/Cp1-118[»]
4WZJX-ray3.60AC/AJ/AQ/BC/BJ/BQ/CC/CJ/CQ/DC/DJ/DQ1-118[»]
5MQFelectron microscopy5.90a/h1-118[»]
5O9Zelectron microscopy4.50S/a/h1-118[»]
5XJCelectron microscopy3.60d/k1-118[»]
ProteinModelPortaliP62316.
SMRiP62316.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP62316.

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP core protein family.Curated

Phylogenomic databases

eggNOGiKOG3459. Eukaryota.
COG1958. LUCA.
GeneTreeiENSGT00390000017608.
HOGENOMiHOG000223545.
HOVERGENiHBG054415.
InParanoidiP62316.
KOiK11096.
OMAiVSKMFLR.
OrthoDBiEOG091G0YU6.
PhylomeDBiP62316.
TreeFamiTF319595.

Family and domain databases

CDDicd01720. Sm_D2. 1 hit.
InterProiView protein in InterPro
IPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
IPR027248. Sm_D2.
PANTHERiPTHR12777. PTHR12777. 1 hit.
PfamiView protein in Pfam
PF01423. LSM. 1 hit.
SMARTiView protein in SMART
SM00651. Sm. 1 hit.
SUPFAMiSSF50182. SSF50182. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P62316-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MSLLNKPKSE MTPEELQKRE EEEFNTGPLS VLTQSVKNNT QVLINCRNNK
60 70 80 90 100
KLLGRVKAFD RHCNMVLENV KEMWTEVPKS GKGKKKSKPV NKDRYISKMF
110
LRGDSVIVVL RNPLIAGK
Length:118
Mass (Da):13,527
Last modified:July 5, 2004 - v1
Checksum:iD986059D82B7E045
GO
Isoform 2 (identifier: P62316-2) [UniParc]FASTAAdd to basket

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

Note: No experimental confirmation available.
Show »
Length:108
Mass (Da):12,399
Checksum:i3E92B3D47F961A7F
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti38N → S in BU531743 (PubMed:15489334).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0453711 – 10Missing in isoform 2. 1 Publication10

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS33053.1. [P62316-1]
CCDS54281.1. [P62316-2]
PIRiI38861.
RefSeqiNP_004588.1. NM_004597.6. [P62316-1]
NP_808210.2. NM_177542.3. [P62316-2]
UniGeneiHs.515472.

Genome annotation databases

EnsembliENST00000342669; ENSP00000342374; ENSG00000125743. [P62316-1]
ENST00000391932; ENSP00000375798; ENSG00000125743. [P62316-2]
ENST00000587367; ENSP00000465952; ENSG00000125743. [P62316-2]
ENST00000588301; ENSP00000465216; ENSG00000125743. [P62316-1]
ENST00000588599; ENSP00000466152; ENSG00000125743. [P62316-2]
GeneIDi6633.
KEGGihsa:6633.
UCSCiuc002pcv.4. human. [P62316-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiSMD2_HUMAN
AccessioniPrimary (citable) accession number: P62316
Secondary accession number(s): A8K797, J3KPM5, P43330
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: October 25, 2017
This is version 151 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families