Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Small nuclear ribonucleoprotein Sm D2

Gene

SNRPD2

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

Functioni

Plays role in pre-mRNA splicing as core component of the SMN-Sm complex that mediates spliceosomal snRNP assembly and as component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:18984161, PubMed:19325628, PubMed:23333303, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Component of both the pre-catalytic spliceosome B complex and activated spliceosome C complexes (PubMed:11991638, PubMed:28502770, PubMed:28781166, PubMed:28076346). Is also a component of the minor U12 spliceosome (PubMed:15146077).10 Publications

Miscellaneous

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

GO - Molecular functioni

GO - Biological processi

  • import into nucleus Source: Reactome
  • mRNA splicing, via spliceosome Source: UniProtKB
  • 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
MIMi601061 gene
neXtProtiNX_P62316

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
ProteomicsDBi57392
TopDownProteomicsiP62316-1 [P62316-1]
P62316-2 [P62316-2]

PTM databases

iPTMnetiP62316
PhosphoSitePlusiP62316
SwissPalmiP62316

Expressioni

Gene expression databases

BgeeiENSG00000125743 Expressed in 236 organ(s), highest expression level in material anatomical entity
CleanExiHS_SNRPD1
HS_SNRPD2
ExpressionAtlasiP62316 baseline and differential
GenevisibleiP62316 HS

Organism-specific databases

HPAiHPA041437

Interactioni

Subunit structurei

Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:19325628, PubMed:21516107, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). 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 (PubMed:10025403, PubMed:19325628, PubMed:21516107, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Component of the U1 snRNP (PubMed:19325628, PubMed:25555158). The U1 snRNP is composed of the U1 snRNA and the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG, and at least three U1 snRNP-specific proteins SNRNP70/U1-70K, SNRPA/U1-A and SNRPC/U1-C (PubMed:19325628, PubMed:25555158). Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 (PubMed:26912367). Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (PubMed:15146077). 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.12 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi112517, 132 interactors
CORUMiP62316
DIPiDIP-31219N
IntActiP62316, 47 interactors
MINTiP62316
STRINGi9606.ENSP00000342374

Structurei

Secondary structure

1118
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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
OMAiMWTEVPR
OrthoDBiEOG091G0YU6
PhylomeDBiP62316
TreeFamiTF319595

Family and domain databases

CDDicd01720 Sm_D2, 1 hit
InterProiView protein in InterPro
IPR001163 LSM_dom_euk/arc
IPR010920 LSM_dom_sf
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

This entry has 2 described isoforms and 2 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
K7EJB5K7EJB5_HUMAN
Small nuclear ribonucleoprotein Sm ...
SNRPD2
54Annotation score:
K7ERG4K7ERG4_HUMAN
Small nuclear ribonucleoprotein Sm ...
SNRPD2
78Annotation score:

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

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[»]
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[»]
5XJLX-ray2.50B1-118[»]
5XJQX-ray3.28B1-118[»]
5XJRX-ray3.12B1-118[»]
5XJSX-ray3.38B1-118[»]
5XJTX-ray2.92B1-118[»]
5XJUX-ray2.58B1-118[»]
5YZGelectron microscopy4.10d/k1-118[»]
5Z56electron microscopy5.10d/k1-118[»]
5Z57electron microscopy6.50d/k1-118[»]
5Z58electron microscopy4.90d/k1-118[»]
ProteinModelPortaliP62316
SMRiP62316
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112517, 132 interactors
CORUMiP62316
DIPiDIP-31219N
IntActiP62316, 47 interactors
MINTiP62316
STRINGi9606.ENSP00000342374

PTM databases

iPTMnetiP62316
PhosphoSitePlusiP62316
SwissPalmiP62316

Polymorphism and mutation databases

BioMutaiSNRPD2
DMDMi51338666

Proteomic databases

EPDiP62316
MaxQBiP62316
PaxDbiP62316
PeptideAtlasiP62316
PRIDEiP62316
ProteomicsDBi57392
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
EuPathDBiHostDB:ENSG00000125743.10
GeneCardsiSNRPD2
HGNCiHGNC:11159 SNRPD2
HPAiHPA041437
MIMi601061 gene
neXtProtiNX_P62316
OpenTargetsiENSG00000125743
PharmGKBiPA36000
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

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
PROiPR:P62316
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000125743 Expressed in 236 organ(s), highest expression level in material anatomical entity
CleanExiHS_SNRPD1
HS_SNRPD2
ExpressionAtlasiP62316 baseline and differential
GenevisibleiP62316 HS

Family and domain databases

CDDicd01720 Sm_D2, 1 hit
InterProiView protein in InterPro
IPR001163 LSM_dom_euk/arc
IPR010920 LSM_dom_sf
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
ProtoNetiSearch...

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: November 7, 2018
This is version 162 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. SIMILARITY comments
    Index of protein domains and families
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.

Do not show this banner again