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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

GO - Molecular functioni

  • poly(A) RNA binding Source: UniProtKB
  • U1 snRNP binding Source: Ensembl

GO - Biological processi

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

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing

Enzyme and pathway databases

BioCyciZFISH:ENSG00000125743-MONOMER.
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

HGNCiHGNC:11159. SNRPD2.

Subcellular locationi

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: UniProtKB
  • cytosol Source: UniProtKB
  • extracellular exosome Source: UniProtKB
  • methylosome Source: UniProtKB
  • nucleoplasm Source: Reactome
  • pICln-Sm protein complex Source: UniProtKB
  • precatalytic spliceosome Source: GO_Central
  • small nuclear ribonucleoprotein complex Source: ProtInc
  • SMN-Sm protein complex Source: UniProtKB
  • spliceosomal complex Source: ProtInc
  • U12-type spliceosomal complex Source: UniProtKB
  • U1 snRNP Source: UniProtKB
  • U2 snRNP Source: GO_Central
  • U4/U6 x U5 tri-snRNP complex Source: GO_Central
  • U4 snRNP Source: UniProtKB
  • U5 snRNP Source: GO_Central
Complete GO annotation...

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
Modified residuei9PhosphoserineCombined sources1
Modified residuei12PhosphothreonineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

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

WithEntry#Exp.IntActNotes
CEP70Q8NHQ13EBI-297993,EBI-739624
CLNS1AP5410510EBI-297993,EBI-724693
LSM2Q9Y3333EBI-297993,EBI-347416
SNRPFP623064EBI-297993,EBI-356900

Protein-protein interaction databases

BioGridi112517. 122 interactors.
DIPiDIP-31219N.
IntActiP62316. 41 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[»]
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.
OMAiCRNNHKL.
OrthoDBiEOG091G0YU6.
PhylomeDBiP62316.
TreeFamiTF319595.

Family and domain databases

InterProiIPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
IPR027248. Sm_D2.
[Graphical view]
PANTHERiPTHR12777. PTHR12777. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
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

Cross-referencesi

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.

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[»]
ProteinModelPortaliP62316.
SMRiP62316.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112517. 122 interactors.
DIPiDIP-31219N.
IntActiP62316. 41 interactors.
MINTiMINT-5002672.
STRINGi9606.ENSP00000342374.

PTM databases

iPTMnetiP62316.
PhosphoSitePlusiP62316.
SwissPalmiP62316.

Polymorphism and mutation databases

BioMutaiSNRPD2.
DMDMi51338666.

Proteomic databases

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

Protocols and materials databases

DNASUi6633.
Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi6633.
GeneCardsiSNRPD2.
HGNCiHGNC:11159. SNRPD2.
HPAiHPA041437.
MIMi601061. gene.
neXtProtiNX_P62316.
OpenTargetsiENSG00000125743.
PharmGKBiPA36000.
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

BioCyciZFISH:ENSG00000125743-MONOMER.
ReactomeiR-HSA-191859. snRNP Assembly.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.

Miscellaneous databases

ChiTaRSiSNRPD2. human.
EvolutionaryTraceiP62316.
GenomeRNAii6633.
PROiP62316.
SOURCEiSearch...

Gene expression databases

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

Family and domain databases

InterProiIPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
IPR027248. Sm_D2.
[Graphical view]
PANTHERiPTHR12777. PTHR12777. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiSMD2_HUMAN
AccessioniPrimary (citable) accession number: P62316
Secondary accession number(s): A8K797, J3KPM5, P43330
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: November 30, 2016
This is version 142 of the entry and version 1 of the sequence. [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

Miscellaneous

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

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.