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 D3

Gene

SNRPD3

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. As part of the U7 snRNP it is involved in histone 3'-end processing.2 Publications

GO - Molecular functioni

  • enzyme binding Source: UniProtKB
  • histone pre-mRNA DCP binding Source: UniProtKB
  • poly(A) RNA binding Source: UniProtKB
  • telomerase RNA binding Source: BHF-UCL
  • U1 snRNP binding Source: Ensembl
  • U2 snRNA binding Source: BHF-UCL
  • U7 snRNA binding Source: BHF-UCL

GO - Biological processi

  • histone mRNA metabolic process Source: Reactome
  • mRNA splicing, via spliceosome Source: UniProtKB
  • nuclear import Source: Reactome
  • protein methylation Source: MGI
  • RNA splicing Source: ProtInc
  • spliceosomal complex assembly Source: GO_Central
  • spliceosomal snRNP assembly Source: UniProtKB
  • termination of RNA polymerase II transcription Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000100028-MONOMER.
ReactomeiR-HSA-109688. Cleavage of Growing Transcript in the Termination Region.
R-HSA-111367. SLBP independent Processing of Histone Pre-mRNAs.
R-HSA-191859. snRNP Assembly.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.
R-HSA-77588. SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs.

Names & Taxonomyi

Protein namesi
Recommended name:
Small nuclear ribonucleoprotein Sm D3
Short name:
Sm-D3
Alternative name(s):
snRNP core protein D3
Gene namesi
Name:SNRPD3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 22

Organism-specific databases

HGNCiHGNC:11160. SNRPD3.

Subcellular locationi

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: UniProtKB
  • commitment complex Source: GO_Central
  • cytoplasm Source: HPA
  • cytosol Source: UniProtKB
  • extracellular exosome Source: UniProtKB
  • methylosome Source: UniProtKB
  • nucleoplasm Source: HPA
  • pICln-Sm protein complex Source: UniProtKB
  • precatalytic spliceosome Source: GO_Central
  • prespliceosome Source: GO_Central
  • small nuclear ribonucleoprotein complex Source: ProtInc
  • SMN-Sm protein complex Source: UniProtKB
  • spliceosomal complex Source: ProtInc
  • spliceosomal tri-snRNP complex Source: GO_Central
  • U12-type spliceosomal complex Source: UniProtKB
  • U1 snRNP Source: UniProtKB
  • U2 snRNP Source: GO_Central
  • U4 snRNP Source: UniProtKB
  • U5 snRNP Source: GO_Central
  • U7 snRNP Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

DisGeNETi6634.
OpenTargetsiENSG00000100028.
PharmGKBiPA36001.

Polymorphism and mutation databases

DMDMi51338667.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00001222142 – 126Small nuclear ribonucleoprotein Sm D3Add BLAST125

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1

Post-translational modificationi

Methylated on arginine residues by PRMT5 and PRMT7; probable asymmetric dimethylation which is required for assembly and biogenesis of snRNPs.2 Publications

Keywords - PTMi

Acetylation, Methylation

Proteomic databases

EPDiP62318.
MaxQBiP62318.
PaxDbiP62318.
PeptideAtlasiP62318.
PRIDEiP62318.
TopDownProteomicsiP62318-1. [P62318-1]

PTM databases

iPTMnetiP62318.
PhosphoSitePlusiP62318.
SwissPalmiP62318.

Expressioni

Gene expression databases

BgeeiENSG00000100028.
CleanExiHS_SNRPD3.
ExpressionAtlasiP62318. baseline and differential.
GenevisibleiP62318. HS.

Organism-specific databases

HPAiHPA001170.

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. Component of the U7 snRNP complex, or U7 Sm protein core complex, at least composed of LSM10, LSM11, SNRPB, SNRPD3, SNRPE, SNRPF, SNRPG and U7 snRNA. 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
CLNS1AP541058EBI-372789,EBI-724693
LSM7Q9UK453EBI-372789,EBI-348372
SNRPBP146782EBI-372789,EBI-372458

GO - Molecular functioni

  • enzyme binding Source: UniProtKB

Protein-protein interaction databases

BioGridi112518. 111 interactors.
DIPiDIP-31216N.
IntActiP62318. 47 interactors.
MINTiMINT-5002679.
STRINGi9606.ENSP00000215829.

Structurei

Secondary structure

1126
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 12Combined sources7
Turni13 – 15Combined sources3
Beta strandi16 – 22Combined sources7
Beta strandi27 – 35Combined sources9
Beta strandi37 – 39Combined sources3
Beta strandi41 – 49Combined sources9
Beta strandi55 – 63Combined sources9
Helixi65 – 67Combined sources3
Beta strandi68 – 73Combined sources6
Helixi75 – 79Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1D3BX-ray2.00A/C/E/G/I/K1-75[»]
3CW1X-ray5.49D/S/T/U1-126[»]
3JCRelectron microscopy7.00R/r1-126[»]
3PGWX-ray4.40W/Z1-126[»]
3VRIX-ray1.60C54-63[»]
4PJOX-ray3.30A/O/a/o1-126[»]
4WZJX-ray3.60AD/AK/AR/BD/BK/BR/CD/CK/CR/DD/DK/DR1-126[»]
ProteinModelPortaliP62318.
SMRiP62318.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP62318.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati110 – 11112
Repeati112 – 11322
Repeati114 – 11532
Repeati116 – 11742
Repeati118 – 11952

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni110 – 1195 X 2 AA tandem repeats of [RM]-G10

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi84 – 126Arg/Lys-rich (basic)Add BLAST43

Sequence similaritiesi

Belongs to the snRNP core protein family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG3172. Eukaryota.
COG1958. LUCA.
GeneTreeiENSGT00610000086153.
HOGENOMiHOG000182712.
HOVERGENiHBG105305.
InParanoidiP62318.
KOiK11088.
OMAiEGHVVTC.
OrthoDBiEOG091G0ZWE.
PhylomeDBiP62318.
TreeFamiTF354302.

Family and domain databases

InterProiIPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
[Graphical view]
PANTHERiPTHR23338. PTHR23338. 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: P62318-1) [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
MSIGVPIKVL HEAEGHIVTC ETNTGEVYRG KLIEAEDNMN CQMSNITVTY
60 70 80 90 100
RDGRVAQLEQ VYIRGSKIRF LILPDMLKNA PMLKSMKNKN QGSGAGRGKA
110 120
AILKAQVAAR GRGRGMGRGN IFQKRR
Length:126
Mass (Da):13,916
Last modified:July 5, 2004 - v1
Checksum:i59A6E78E860AA3E0
GO
Isoform 2 (identifier: P62318-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     107-126: VAARGRGRGMGRGNIFQKRR → GYLSSLEWVLVHIC

Note: No experimental confirmation available.
Show »
Length:120
Mass (Da):13,292
Checksum:iFAEF4075E9ED6E9D
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_056478107 – 126VAARG…FQKRR → GYLSSLEWVLVHIC in isoform 2. 1 PublicationAdd BLAST20

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U15009 mRNA. Translation: AAA57034.1.
CR456583 mRNA. Translation: CAG30469.1.
AK296173 mRNA. Translation: BAG58909.1.
AB451249 mRNA. Translation: BAG70063.1.
AB451373 mRNA. Translation: BAG70187.1.
AP000356 Genomic DNA. No translation available.
CH471095 Genomic DNA. Translation: EAW59670.1.
BC000457 mRNA. Translation: AAH00457.1.
BC003150 mRNA. Translation: AAH03150.1.
CCDSiCCDS13828.1. [P62318-1]
RefSeqiNP_001265585.1. NM_001278656.1. [P62318-1]
NP_004166.1. NM_004175.4. [P62318-1]
UniGeneiHs.356549.

Genome annotation databases

EnsembliENST00000215829; ENSP00000215829; ENSG00000100028. [P62318-1]
ENST00000402849; ENSP00000385266; ENSG00000100028. [P62318-2]
ENST00000404603; ENSP00000456090; ENSG00000100028. [P62318-1]
GeneIDi6634.
KEGGihsa:6634.
UCSCiuc003aam.3. human. [P62318-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U15009 mRNA. Translation: AAA57034.1.
CR456583 mRNA. Translation: CAG30469.1.
AK296173 mRNA. Translation: BAG58909.1.
AB451249 mRNA. Translation: BAG70063.1.
AB451373 mRNA. Translation: BAG70187.1.
AP000356 Genomic DNA. No translation available.
CH471095 Genomic DNA. Translation: EAW59670.1.
BC000457 mRNA. Translation: AAH00457.1.
BC003150 mRNA. Translation: AAH03150.1.
CCDSiCCDS13828.1. [P62318-1]
RefSeqiNP_001265585.1. NM_001278656.1. [P62318-1]
NP_004166.1. NM_004175.4. [P62318-1]
UniGeneiHs.356549.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1D3BX-ray2.00A/C/E/G/I/K1-75[»]
3CW1X-ray5.49D/S/T/U1-126[»]
3JCRelectron microscopy7.00R/r1-126[»]
3PGWX-ray4.40W/Z1-126[»]
3VRIX-ray1.60C54-63[»]
4PJOX-ray3.30A/O/a/o1-126[»]
4WZJX-ray3.60AD/AK/AR/BD/BK/BR/CD/CK/CR/DD/DK/DR1-126[»]
ProteinModelPortaliP62318.
SMRiP62318.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112518. 111 interactors.
DIPiDIP-31216N.
IntActiP62318. 47 interactors.
MINTiMINT-5002679.
STRINGi9606.ENSP00000215829.

PTM databases

iPTMnetiP62318.
PhosphoSitePlusiP62318.
SwissPalmiP62318.

Polymorphism and mutation databases

DMDMi51338667.

Proteomic databases

EPDiP62318.
MaxQBiP62318.
PaxDbiP62318.
PeptideAtlasiP62318.
PRIDEiP62318.
TopDownProteomicsiP62318-1. [P62318-1]

Protocols and materials databases

DNASUi6634.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000215829; ENSP00000215829; ENSG00000100028. [P62318-1]
ENST00000402849; ENSP00000385266; ENSG00000100028. [P62318-2]
ENST00000404603; ENSP00000456090; ENSG00000100028. [P62318-1]
GeneIDi6634.
KEGGihsa:6634.
UCSCiuc003aam.3. human. [P62318-1]

Organism-specific databases

CTDi6634.
DisGeNETi6634.
GeneCardsiSNRPD3.
HGNCiHGNC:11160. SNRPD3.
HPAiHPA001170.
MIMi601062. gene.
neXtProtiNX_P62318.
OpenTargetsiENSG00000100028.
PharmGKBiPA36001.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3172. Eukaryota.
COG1958. LUCA.
GeneTreeiENSGT00610000086153.
HOGENOMiHOG000182712.
HOVERGENiHBG105305.
InParanoidiP62318.
KOiK11088.
OMAiEGHVVTC.
OrthoDBiEOG091G0ZWE.
PhylomeDBiP62318.
TreeFamiTF354302.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000100028-MONOMER.
ReactomeiR-HSA-109688. Cleavage of Growing Transcript in the Termination Region.
R-HSA-111367. SLBP independent Processing of Histone Pre-mRNAs.
R-HSA-191859. snRNP Assembly.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.
R-HSA-77588. SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs.

Miscellaneous databases

ChiTaRSiSNRPD3. human.
EvolutionaryTraceiP62318.
GeneWikiiSNRPD3.
GenomeRNAii6634.
PROiP62318.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000100028.
CleanExiHS_SNRPD3.
ExpressionAtlasiP62318. baseline and differential.
GenevisibleiP62318. HS.

Family and domain databases

InterProiIPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
[Graphical view]
PANTHERiPTHR23338. PTHR23338. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiSMD3_HUMAN
AccessioniPrimary (citable) accession number: P62318
Secondary accession number(s): B4DJP7, B5BU13, P43331
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: November 30, 2016
This is version 139 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 22
    Human chromosome 22: 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.