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Protein

Small nuclear ribonucleoprotein Sm D1

Gene

SNRPD1

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. May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through nonspecific electrostatic contacts with RNA.2 Publications

GO - Molecular functioni

  • poly(A) RNA binding Source: UniProtKB
  • RNA binding Source: ProtInc
  • 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:ENSG00000167088-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 D1
Short name:
Sm-D1
Alternative name(s):
Sm-D autoantigen
snRNP core protein D1
Gene namesi
Name:SNRPD1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 18

Organism-specific databases

HGNCiHGNC:11158. SNRPD1.

Subcellular locationi

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: UniProtKB
  • commitment complex Source: GO_Central
  • cytosol Source: UniProtKB
  • methylosome Source: UniProtKB
  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
  • 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 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
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi58L → K: Loss of interaction with CLNS1A. 1 Publication1
Mutagenesisi60I → R: Loss of interaction with CLNS1A. 1 Publication1

Organism-specific databases

DisGeNETi6632.
OpenTargetsiENSG00000167088.
PharmGKBiPA164742464.

Polymorphism and mutation databases

BioMutaiSNRPD1.
DMDMi51338665.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001222011 – 119Small nuclear ribonucleoprotein Sm D1Add BLAST119

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

Methylation

Proteomic databases

EPDiP62314.
MaxQBiP62314.
PaxDbiP62314.
PeptideAtlasiP62314.
PRIDEiP62314.
TopDownProteomicsiP62314.

PTM databases

iPTMnetiP62314.
PhosphoSitePlusiP62314.
SwissPalmiP62314.

Expressioni

Gene expression databases

BgeeiENSG00000167088.
CleanExiHS_SNRPD1.
ExpressionAtlasiP62314. baseline and differential.
GenevisibleiP62314. HS.

Organism-specific databases

HPAiHPA040516.

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
P279587EBI-372177,EBI-3649474From a different organism.
CLNS1AP5410511EBI-372177,EBI-724693

Protein-protein interaction databases

BioGridi112516. 139 interactors.
DIPiDIP-31207N.
IntActiP62314. 48 interactors.
MINTiMINT-1530147.
STRINGi9606.ENSP00000300413.

Structurei

Secondary structure

1119
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 8Combined sources6
Beta strandi14 – 19Combined sources6
Beta strandi24 – 32Combined sources9
Beta strandi38 – 46Combined sources9
Beta strandi53 – 60Combined sources8
Helixi62 – 64Combined sources3
Beta strandi65 – 69Combined sources5
Helixi76 – 79Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1B34X-ray2.50A1-119[»]
3CW1X-ray5.49B/M/N/O1-119[»]
3JCRelectron microscopy7.00P/p1-119[»]
3PGWX-ray4.40U/X1-119[»]
3S6NX-ray2.50A1-119[»]
4F7UX-ray1.90A/C1-119[»]
4PJOX-ray3.30C/Q/c/q2-85[»]
4V98X-ray3.10AA/AI/AQ/AY/Ag/Ao/Aw/BA/BI/BQ/BY/Bg/Bo/Bw/CA/CI/CQ/CY/Cg/Co1-119[»]
4WZJX-ray3.60AB/AI/AP/BB/BI/BP/CB/CI/CP/DB/DI/DP1-119[»]
ProteinModelPortaliP62314.
SMRiP62314.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP62314.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 80Sufficient for interaction with CLNS1A1 PublicationAdd BLAST80

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi86 – 119Arg/Lys-rich (basic)Add BLAST34

Sequence similaritiesi

Belongs to the snRNP core protein family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG3428. Eukaryota.
COG1958. LUCA.
GeneTreeiENSGT00510000047245.
HOGENOMiHOG000182713.
HOVERGENiHBG061491.
InParanoidiP62314.
KOiK11087.
OMAiQMNTALR.
OrthoDBiEOG091G11O6.
PhylomeDBiP62314.
TreeFamiTF314224.

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.

Sequencei

Sequence statusi: Complete.

P62314-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLVRFLMKL SHETVTIELK NGTQVHGTIT GVDVSMNTHL KAVKMTLKNR
60 70 80 90 100
EPVQLETLSI RGNNIRYFIL PDSLPLDTLL VDVEPKVKSK KREAVAGRGR
110
GRGRGRGRGR GRGRGGPRR
Length:119
Mass (Da):13,282
Last modified:July 5, 2004 - v1
Checksum:i0C81C94BF98E0810
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03798 mRNA. Translation: AAA36620.1.
L36188
, L36182, L36186, L36187 Genomic DNA. Translation: AAA85339.1.
CR542239 mRNA. Translation: CAG47035.1.
AB451227 mRNA. Translation: BAG70041.1.
AB451350 mRNA. Translation: BAG70164.1.
CH471088 Genomic DNA. Translation: EAX01130.1.
BC001721 mRNA. Translation: AAH01721.1.
BC072427 mRNA. Translation: AAH72427.1.
CCDSiCCDS32801.1.
PIRiA94201. A27668.
RefSeqiNP_001278845.1. NM_001291916.1.
NP_008869.1. NM_006938.3.
UniGeneiHs.464734.

Genome annotation databases

EnsembliENST00000300413; ENSP00000300413; ENSG00000167088.
GeneIDi6632.
KEGGihsa:6632.
UCSCiuc002ktj.2. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03798 mRNA. Translation: AAA36620.1.
L36188
, L36182, L36186, L36187 Genomic DNA. Translation: AAA85339.1.
CR542239 mRNA. Translation: CAG47035.1.
AB451227 mRNA. Translation: BAG70041.1.
AB451350 mRNA. Translation: BAG70164.1.
CH471088 Genomic DNA. Translation: EAX01130.1.
BC001721 mRNA. Translation: AAH01721.1.
BC072427 mRNA. Translation: AAH72427.1.
CCDSiCCDS32801.1.
PIRiA94201. A27668.
RefSeqiNP_001278845.1. NM_001291916.1.
NP_008869.1. NM_006938.3.
UniGeneiHs.464734.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1B34X-ray2.50A1-119[»]
3CW1X-ray5.49B/M/N/O1-119[»]
3JCRelectron microscopy7.00P/p1-119[»]
3PGWX-ray4.40U/X1-119[»]
3S6NX-ray2.50A1-119[»]
4F7UX-ray1.90A/C1-119[»]
4PJOX-ray3.30C/Q/c/q2-85[»]
4V98X-ray3.10AA/AI/AQ/AY/Ag/Ao/Aw/BA/BI/BQ/BY/Bg/Bo/Bw/CA/CI/CQ/CY/Cg/Co1-119[»]
4WZJX-ray3.60AB/AI/AP/BB/BI/BP/CB/CI/CP/DB/DI/DP1-119[»]
ProteinModelPortaliP62314.
SMRiP62314.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112516. 139 interactors.
DIPiDIP-31207N.
IntActiP62314. 48 interactors.
MINTiMINT-1530147.
STRINGi9606.ENSP00000300413.

PTM databases

iPTMnetiP62314.
PhosphoSitePlusiP62314.
SwissPalmiP62314.

Polymorphism and mutation databases

BioMutaiSNRPD1.
DMDMi51338665.

Proteomic databases

EPDiP62314.
MaxQBiP62314.
PaxDbiP62314.
PeptideAtlasiP62314.
PRIDEiP62314.
TopDownProteomicsiP62314.

Protocols and materials databases

DNASUi6632.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000300413; ENSP00000300413; ENSG00000167088.
GeneIDi6632.
KEGGihsa:6632.
UCSCiuc002ktj.2. human.

Organism-specific databases

CTDi6632.
DisGeNETi6632.
GeneCardsiSNRPD1.
HGNCiHGNC:11158. SNRPD1.
HPAiHPA040516.
MIMi601063. gene.
neXtProtiNX_P62314.
OpenTargetsiENSG00000167088.
PharmGKBiPA164742464.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3428. Eukaryota.
COG1958. LUCA.
GeneTreeiENSGT00510000047245.
HOGENOMiHOG000182713.
HOVERGENiHBG061491.
InParanoidiP62314.
KOiK11087.
OMAiQMNTALR.
OrthoDBiEOG091G11O6.
PhylomeDBiP62314.
TreeFamiTF314224.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000167088-MONOMER.
ReactomeiR-HSA-191859. snRNP Assembly.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.

Miscellaneous databases

ChiTaRSiSNRPD1. human.
EvolutionaryTraceiP62314.
GeneWikiiSmall_nuclear_ribonucleoprotein_D1.
GenomeRNAii6632.
PROiP62314.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000167088.
CleanExiHS_SNRPD1.
ExpressionAtlasiP62314. baseline and differential.
GenevisibleiP62314. 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 nameiSMD1_HUMAN
AccessioniPrimary (citable) accession number: P62314
Secondary accession number(s): B5BTZ1, P13641
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 18
    Human chromosome 18: 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.