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Protein

Small nuclear ribonucleoprotein Sm D1

Gene

SNRPD1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

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: 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 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

EuPathDBiHostDB:ENSG00000167088.10
HGNCiHGNC:11158 SNRPD1
MIMi601063 gene
neXtProtiNX_P62314

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

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

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki86Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

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

Isopeptide bond, Methylation, Ubl conjugation

Proteomic databases

EPDiP62314
MaxQBiP62314
PaxDbiP62314
PeptideAtlasiP62314
PRIDEiP62314
ProteomicsDBi57391
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

Show more details

Protein-protein interaction databases

BioGridi112516, 150 interactors
CORUMiP62314
DIPiDIP-31207N
IntActiP62314, 52 interactors
MINTiP62314
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[»]
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[»]
5MQFelectron microscopy5.90g/n1-119[»]
5O9Zelectron microscopy4.50Z/g/n1-119[»]
5XJCelectron microscopy3.60c/j1-119[»]
5XJLX-ray2.50A1-119[»]
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
OMAiPQMNTAL
OrthoDBiEOG091G11O6
PhylomeDBiP62314
TreeFamiTF314224

Family and domain databases

CDDicd01724 Sm_D1, 1 hit
InterProiView protein in InterPro
IPR027141 LSm4/Sm_D1/D3
IPR001163 LSM_dom_euk/arc
IPR010920 LSM_dom_sf
IPR034102 Sm_D1
PANTHERiPTHR23338 PTHR23338, 1 hit
PfamiView protein in Pfam
PF01423 LSM, 1 hit
SMARTiView protein in SMART
SM00651 Sm, 1 hit
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

Similar proteinsi

Entry informationi

Entry nameiSMD1_HUMAN
AccessioniPrimary (citable) accession number: P62314
Secondary accession number(s): B5BTZ1, P13641
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: June 20, 2018
This is version 156 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

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