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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 an 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

GO - Biological processi

  • activation of mitophagy in response to mitochondrial depolarization Source: ParkinsonsUK-UCL
  • gene expression Source: Reactome
  • mRNA splicing, via spliceosome Source: UniProtKB
  • ncRNA metabolic process Source: Reactome
  • positive regulation of defense response to virus by host Source: ParkinsonsUK-UCL
  • RNA splicing Source: Reactome
  • 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

ReactomeiREACT_11066. snRNP Assembly.
REACT_1753. mRNA Splicing - Minor Pathway.
REACT_467. mRNA Splicing - Major 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
ProteomesiUP000005640 Componenti: Chromosome 18

Organism-specific databases

HGNCiHGNC:11158. SNRPD1.

Subcellular locationi

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: UniProtKB
  • cytosol Source: UniProtKB
  • methylosome Source: UniProtKB
  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
  • pICln-Sm protein complex Source: UniProtKB
  • small nuclear ribonucleoprotein complex Source: ProtInc
  • SMN-Sm protein complex Source: UniProtKB
  • U12-type spliceosomal complex Source: UniProtKB
  • U1 snRNP Source: UniProtKB
  • U4 snRNP Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi58 – 581L → K: Loss of interaction with CLNS1A. 1 Publication
Mutagenesisi60 – 601I → R: Loss of interaction with CLNS1A. 1 Publication

Organism-specific databases

PharmGKBiPA164742464.

Polymorphism and mutation databases

BioMutaiSNRPD1.
DMDMi51338665.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 119119Small nuclear ribonucleoprotein Sm D1PRO_0000122201Add
BLAST

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

MaxQBiP62314.
PaxDbiP62314.
PeptideAtlasiP62314.
PRIDEiP62314.

PTM databases

PhosphoSiteiP62314.

Expressioni

Gene expression databases

BgeeiP62314.
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 an 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.
CLNS1AP541059EBI-372177,EBI-724693

Protein-protein interaction databases

BioGridi112516. 116 interactions.
DIPiDIP-31207N.
IntActiP62314. 42 interactions.
MINTiMINT-1530147.
STRINGi9606.ENSP00000300413.

Structurei

Secondary structure

1
119
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 86Combined sources
Beta strandi14 – 196Combined sources
Beta strandi24 – 329Combined sources
Beta strandi38 – 469Combined sources
Beta strandi53 – 608Combined sources
Helixi62 – 643Combined sources
Beta strandi65 – 695Combined sources
Helixi76 – 794Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1B34X-ray2.50A1-119[»]
3CW1X-ray5.49B/M/N/O1-119[»]
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. Positions 1-82.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP62314.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 8080Sufficient for interaction with CLNS1AAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi86 – 11934Arg/Lys-rich (basic)Add
BLAST

Sequence similaritiesi

Belongs to the snRNP core protein family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG1958.
GeneTreeiENSGT00510000047245.
HOGENOMiHOG000182713.
HOVERGENiHBG061491.
InParanoidiP62314.
KOiK11087.
OMAiQMNTALR.
OrthoDBiEOG7BZVWB.
PhylomeDBiP62314.
TreeFamiTF314224.

Family and domain databases

InterProiIPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_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.1. 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
EntryMethodResolution (Å)ChainPositionsPDBsum
1B34X-ray2.50A1-119[»]
3CW1X-ray5.49B/M/N/O1-119[»]
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. Positions 1-82.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112516. 116 interactions.
DIPiDIP-31207N.
IntActiP62314. 42 interactions.
MINTiMINT-1530147.
STRINGi9606.ENSP00000300413.

PTM databases

PhosphoSiteiP62314.

Polymorphism and mutation databases

BioMutaiSNRPD1.
DMDMi51338665.

Proteomic databases

MaxQBiP62314.
PaxDbiP62314.
PeptideAtlasiP62314.
PRIDEiP62314.

Protocols and materials databases

DNASUi6632.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000300413; ENSP00000300413; ENSG00000167088.
GeneIDi6632.
KEGGihsa:6632.
UCSCiuc002ktj.1. human.

Organism-specific databases

CTDi6632.
GeneCardsiGC18P019192.
HGNCiHGNC:11158. SNRPD1.
HPAiHPA040516.
MIMi601063. gene.
neXtProtiNX_P62314.
PharmGKBiPA164742464.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG1958.
GeneTreeiENSGT00510000047245.
HOGENOMiHOG000182713.
HOVERGENiHBG061491.
InParanoidiP62314.
KOiK11087.
OMAiQMNTALR.
OrthoDBiEOG7BZVWB.
PhylomeDBiP62314.
TreeFamiTF314224.

Enzyme and pathway databases

ReactomeiREACT_11066. snRNP Assembly.
REACT_1753. mRNA Splicing - Minor Pathway.
REACT_467. mRNA Splicing - Major Pathway.

Miscellaneous databases

ChiTaRSiSNRPD1. human.
EvolutionaryTraceiP62314.
GeneWikiiSmall_nuclear_ribonucleoprotein_D1.
GenomeRNAii6632.
NextBioi25835.
PROiP62314.
SOURCEiSearch...

Gene expression databases

BgeeiP62314.
CleanExiHS_SNRPD1.
ExpressionAtlasiP62314. baseline and differential.
GenevisibleiP62314. HS.

Family and domain databases

InterProiIPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_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...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular cloning of a cDNA encoding the human Sm-D autoantigen."
    Rokeach L.A., Haselby J.A., Hoch S.O.
    Proc. Natl. Acad. Sci. U.S.A. 85:4832-4836(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 1-11.
    Tissue: Placenta.
  2. Rokeach L.A.
    Submitted (JUL-1988) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION.
  3. "Expression of the major human ribonucleoprotein (RNP) autoantigens in Escherichia coli and their use in an EIA for screening sera from patients with autoimmune diseases."
    Renz M., Heim C., Braeunling O., Czichos A., Wieland C., Seelig H.P.
    Clin. Chem. 35:1861-1863(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  4. "Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
    Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
    Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "Human protein factory for converting the transcriptome into an in vitro-expressed proteome."
    Goshima N., Kawamura Y., Fukumoto A., Miura A., Honma R., Satoh R., Wakamatsu A., Yamamoto J., Kimura K., Nishikawa T., Andoh T., Iida Y., Ishikawa K., Ito E., Kagawa N., Kaminaga C., Kanehori K., Kawakami B.
    , Kenmochi K., Kimura R., Kobayashi M., Kuroita T., Kuwayama H., Maruyama Y., Matsuo K., Minami K., Mitsubori M., Mori M., Morishita R., Murase A., Nishikawa A., Nishikawa S., Okamoto T., Sakagami N., Sakamoto Y., Sasaki Y., Seki T., Sono S., Sugiyama A., Sumiya T., Takayama T., Takayama Y., Takeda H., Togashi T., Yahata K., Yamada H., Yanagisawa Y., Endo Y., Imamoto F., Kisu Y., Tanaka S., Isogai T., Imai J., Watanabe S., Nomura N.
    Nat. Methods 5:1011-1017(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  7. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Eye.
  8. "Methylation of Sm proteins by a complex containing PRMT5 and the putative U snRNP assembly factor pICln."
    Meister G., Eggert C., Buehler D., Brahms H., Kambach C., Fischer U.
    Curr. Biol. 11:1990-1994(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: METHYLATION, INTERACTION WITH CLNS1A, MUTAGENESIS OF LEU-58 AND ILE-60.
  9. "Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis."
    Jurica M.S., Licklider L.J., Gygi S.P., Grigorieff N., Moore M.J.
    RNA 8:426-439(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE SPLICEOSOMAL C COMPLEX.
  10. "The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome."
    Will C.L., Schneider C., Hossbach M., Urlaub H., Rauhut R., Elbashir S., Tuschl T., Luehrmann R.
    RNA 10:929-941(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN A COMPLEX WITH THE U11/U12 SPLICEOSOME, IDENTIFICATION BY MASS SPECTROMETRY.
  11. "Two distinct arginine methyltransferases are required for biogenesis of Sm-class ribonucleoproteins."
    Gonsalvez G.B., Tian L., Ospina J.K., Boisvert F.-M., Lamond A.I., Matera A.G.
    J. Cell Biol. 178:733-740(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: METHYLATION, INTERACTION WITH PRMT5 AND PRMT7.
  12. "An assembly chaperone collaborates with the SMN complex to generate spliceosomal SnRNPs."
    Chari A., Golas M.M., Klingenhager M., Neuenkirchen N., Sander B., Englbrecht C., Sickmann A., Stark H., Fischer U.
    Cell 135:497-509(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN SNRNP BIOGENESIS, IDENTIFICATION IN 6S PICLN-SM COMPLEX, IDENTIFICATION IN SMN-SM COMPLEX, SUBCELLULAR LOCATION.
  13. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  14. "Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs."
    Kambach C., Walke S., Young R., Avis J.M., de la Fortelle E., Raker V.A., Luehrmann R., Li J., Nagai K.
    Cell 96:375-387(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 2-81 IN COMPLEX WITH SNRPD2.
  15. "Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution."
    Pomeranz Krummel D.A., Oubridge C., Leung A.K., Li J., Nagai K.
    Nature 458:475-480(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (5.49 ANGSTROMS) IN SPLICEOSOMAL U1 SNRNP.
  16. "Functional organization of the Sm core in the crystal structure of human U1 snRNP."
    Weber G., Trowitzsch S., Kastner B., Luhrmann R., Wahl M.C.
    EMBO J. 29:4172-4184(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (4.40 ANGSTROMS) IN SPLICEOSOMAL U1 SNRNP.
  17. "Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis."
    Leung A.K., Nagai K., Li J.
    Nature 473:536-539(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.60 ANGSTROMS) IN SPLICEOSOMAL CORE U4 SNRNP.
  18. "Structural basis of assembly chaperone-mediated snRNP formation."
    Grimm C., Chari A., Pelz J.P., Kuper J., Kisker C., Diederichs K., Stark H., Schindelin H., Fischer U.
    Mol. Cell 49:692-703(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN 6S PICLN-SM COMPLEX, IDENTIFICATION IN 6S PICLN-SM COMPLEX, FUNCTION IN CORE U1 SNRNP BIOGENESIS.

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: June 24, 2015
This is version 128 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

External Data

Dasty 3

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 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.