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P62314

- SMD1_HUMAN

UniProt

P62314 - SMD1_HUMAN

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Protein
Small nuclear ribonucleoprotein Sm D1
Gene
SNRPD1
Organism
Homo sapiens (Human)
Status
Reviewed - 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

  1. RNA binding Source: ProtInc
  2. poly(A) RNA binding Source: UniProtKB
  3. protein binding Source: UniProtKB

GO - Biological processi

  1. RNA metabolic process Source: Reactome
  2. RNA splicing Source: Reactome
  3. gene expression Source: Reactome
  4. mRNA splicing, via spliceosome Source: UniProtKB
  5. ncRNA metabolic process Source: Reactome
  6. spliceosomal complex assembly Source: ProtInc
  7. 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: Chromosome 18

Organism-specific databases

HGNCiHGNC:11158. SNRPD1.

Subcellular locationi

Cytoplasmcytosol. Nucleus
Note: SMN-mediated assembly into core snRNPs occurs in the cytosol before SMN-mediated transport to the nucleus to be included in spliceosomes.1 Publication

GO - Cellular componenti

  1. SMN-Sm protein complex Source: UniProtKB
  2. U1 snRNP Source: UniProtKB
  3. U12-type spliceosomal complex Source: UniProtKB
  4. U4 snRNP Source: UniProtKB
  5. catalytic step 2 spliceosome Source: UniProtKB
  6. cytosol Source: UniProtKB
  7. methylosome Source: UniProtKB
  8. nucleoplasm Source: Reactome
  9. nucleus Source: UniProt
  10. pICln-Sm protein complex Source: UniProtKB
  11. small nuclear ribonucleoprotein complex Source: ProtInc
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.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 119119Small nuclear ribonucleoprotein Sm D1
PRO_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

ArrayExpressiP62314.
BgeeiP62314.
CleanExiHS_SNRPD1.
GenevestigatoriP62314.

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.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CLNS1AP541056EBI-372177,EBI-724693

Protein-protein interaction databases

BioGridi112516. 112 interactions.
DIPiDIP-31207N.
IntActiP62314. 39 interactions.
MINTiMINT-1530147.
STRINGi9606.ENSP00000300413.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 86
Turni9 – 124
Beta strandi14 – 196
Beta strandi24 – 329
Beta strandi38 – 469
Beta strandi53 – 608
Helixi62 – 643
Beta strandi65 – 695
Helixi76 – 794

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1B34X-ray2.50A1-119[»]
1VU2X-ray3.10A/I/Q/Y/g/o/w1-119[»]
1VU3X-ray3.10A/I/Q/Y/g/o1-119[»]
2Y9AX-ray3.60B/I/P1-119[»]
2Y9BX-ray3.60B/I/P1-119[»]
2Y9CX-ray3.60B/I/P1-119[»]
2Y9DX-ray3.60B/I/P1-119[»]
3CW1X-ray5.49B/M/N/O1-119[»]
3PGWX-ray4.40U/X1-119[»]
3S6NX-ray2.50A1-119[»]
4F77X-ray3.10A/I/Q/Y/g/o/w1-119[»]
4F7UX-ray1.90A/C1-119[»]
ProteinModelPortaliP62314.
SMRiP62314. Positions 1-96.

Miscellaneous databases

EvolutionaryTraceiP62314.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 8080Sufficient for interaction with CLNS1A
Add
BLAST

Compositional bias

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

Sequence similaritiesi

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG1958.
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

MKLVRFLMKL SHETVTIELK NGTQVHGTIT GVDVSMNTHL KAVKMTLKNR    50
EPVQLETLSI RGNNIRYFIL PDSLPLDTLL VDVEPKVKSK KREAVAGRGR 100
GRGRGRGRGR GRGRGGPRR 119
Length:119
Mass (Da):13,282
Last modified:July 5, 2004 - v1
Checksum:i0C81C94BF98E0810
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.

Polymorphism databases

DMDMi51338665.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS32801.1.
PIRi A94201. A27668.
RefSeqi NP_001278845.1. NM_001291916.1.
NP_008869.1. NM_006938.3.
UniGenei Hs.464734.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1B34 X-ray 2.50 A 1-119 [» ]
1VU2 X-ray 3.10 A/I/Q/Y/g/o/w 1-119 [» ]
1VU3 X-ray 3.10 A/I/Q/Y/g/o 1-119 [» ]
2Y9A X-ray 3.60 B/I/P 1-119 [» ]
2Y9B X-ray 3.60 B/I/P 1-119 [» ]
2Y9C X-ray 3.60 B/I/P 1-119 [» ]
2Y9D X-ray 3.60 B/I/P 1-119 [» ]
3CW1 X-ray 5.49 B/M/N/O 1-119 [» ]
3PGW X-ray 4.40 U/X 1-119 [» ]
3S6N X-ray 2.50 A 1-119 [» ]
4F77 X-ray 3.10 A/I/Q/Y/g/o/w 1-119 [» ]
4F7U X-ray 1.90 A/C 1-119 [» ]
ProteinModelPortali P62314.
SMRi P62314. Positions 1-96.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 112516. 112 interactions.
DIPi DIP-31207N.
IntActi P62314. 39 interactions.
MINTi MINT-1530147.
STRINGi 9606.ENSP00000300413.

PTM databases

PhosphoSitei P62314.

Polymorphism databases

DMDMi 51338665.

Proteomic databases

MaxQBi P62314.
PaxDbi P62314.
PeptideAtlasi P62314.
PRIDEi P62314.

Protocols and materials databases

DNASUi 6632.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000300413 ; ENSP00000300413 ; ENSG00000167088 .
GeneIDi 6632.
KEGGi hsa:6632.
UCSCi uc002ktj.1. human.

Organism-specific databases

CTDi 6632.
GeneCardsi GC18P019192.
HGNCi HGNC:11158. SNRPD1.
HPAi HPA040516.
MIMi 601063. gene.
neXtProti NX_P62314.
PharmGKBi PA164742464.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG1958.
HOGENOMi HOG000182713.
HOVERGENi HBG061491.
InParanoidi P62314.
KOi K11087.
OMAi QMNTALR.
OrthoDBi EOG7BZVWB.
PhylomeDBi P62314.
TreeFami TF314224.

Enzyme and pathway databases

Reactomei REACT_11066. snRNP Assembly.
REACT_1753. mRNA Splicing - Minor Pathway.
REACT_467. mRNA Splicing - Major Pathway.

Miscellaneous databases

ChiTaRSi SNRPD1. human.
EvolutionaryTracei P62314.
GeneWikii Small_nuclear_ribonucleoprotein_D1.
GenomeRNAii 6632.
NextBioi 25835.
PROi P62314.
SOURCEi Search...

Gene expression databases

ArrayExpressi P62314.
Bgeei P62314.
CleanExi HS_SNRPD1.
Genevestigatori P62314.

Family and domain databases

InterProi IPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view ]
PANTHERi PTHR23338. PTHR23338. 1 hit.
Pfami PF01423. LSM. 1 hit.
[Graphical view ]
SMARTi SM00651. Sm. 1 hit.
[Graphical view ]
SUPFAMi SSF50182. SSF50182. 1 hit.
ProtoNeti Search...

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: September 3, 2014
This is version 120 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

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