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UniProtKB - Q02260 (SMD1_YEAST)

Entry version 181 (02 Dec 2020)
Sequence version 1 (01 Oct 1993)
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Protein

Small nuclear ribonucleoprotein Sm D1

Gene

SMD1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Also binds telomerase RNA and is required for its accumulation.2 Publications

Miscellaneous

Present with 2400 molecules/cell in log phase SD medium.1 Publication

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

  • mRNA binding Source: SGD
  • RNA binding Source: GO_Central
Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionRibonucleoprotein, RNA-binding
Biological processmRNA processing, mRNA splicing

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Small nuclear ribonucleoprotein Sm D1
Short name:
Sm-D1
Alternative name(s):
snRNP core protein D1
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:SMD1
Ordered Locus Names:YGR074W
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri559292 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002311 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome VII

Organism-specific databases

Eukaryotic Pathogen and Host Database Resources

More...EuPathDBi		FungiDB:YGR074W

Saccharomyces Genome Database

More...SGDi		S000003306, SMD1

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001222061 – 146Small nuclear ribonucleoprotein Sm D1Add BLAST146

Proteomic databases

MaxQB - The MaxQuant DataBase

More...MaxQBi		Q02260

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		Q02260

PRoteomics IDEntifications database

More...PRIDEi		Q02260

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Component of the Sm core complex, present in spliceosomal snRNP U1, U2, U4/U6 and U5. The core complex contains SMB1, SMD1, SMD2, SMD3, SME1, SMX3 and SMX2 (Sm proteins B, D1, D2, D3, E, F and G, respectively), and is probably a heptameric ring structure. Belongs to the CWC complex (or CEF1-associated complex), a spliceosome sub-complex reminiscent of a late-stage spliceosome composed of the U2, U5 and U6 snRNAs and at least BUD13, BUD31, BRR2, CDC40, CEF1, CLF1, CUS1, CWC2, CWC15, CWC21, CWC22, CWC23, CWC24, CWC25, CWC27, ECM2, HSH155, IST3, ISY1, LEA1, MSL1, NTC20, PRP8, PRP9, PRP11, PRP19, PRP21, PRP22, PRP45, PRP46, SLU7, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, SNT309, SNU114, SPP2, SYF1, SYF2, RSE1 and YJU2.

Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRP3, PRP4, PRP6, PRP8, PRP18, PRP31, PRP38, SNU13, SNU23, SNU66, SNU114, SPP381, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, LSM8, BRR2 and DIB1.

3 Publications

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		33316, 382 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...ComplexPortali		CPX-1651, PRP19-associated complex
CPX-23, U1 snRNP
CPX-25, U4/U6.U5 tri-snRNP complex
CPX-26, U2 snRNP
CPX-29, U5 snRNP
CPX-30, AAR2-U5 snRNP
CPX-31, U4 snRNP
CPX-32, U4/U6 snRNP
CPX-43, Sm complex

Database of interacting proteins

More...DIPi		DIP-227N

Protein interaction database and analysis system

More...IntActi		Q02260, 26 interactors

Molecular INTeraction database

More...MINTi		Q02260

STRING: functional protein association networks

More...STRINGi		4932.YGR074W

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...RNActi		Q02260, protein

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1146
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		Q02260

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a short (usually not more than 20 amino acids) conserved sequence motif of biological significance.<p><a href='/help/motif' target='_top'>More...</a></p>Motifi128 – 144Nuclear localization signalSequence analysisAdd BLAST17

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

C-terminal extension may function as a nuclear localization signal (NLS).

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the snRNP core protein family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		KOG3428, Eukaryota

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_123956_2_0_1

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		Q02260

Identification of Orthologs from Complete Genome Data

More...OMAi		TVSPQMN

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR027141, LSm4/Sm_D1/D3
IPR001163, LSM_dom_euk/arc
IPR010920, LSM_dom_sf

The PANTHER Classification System

More...PANTHERi		PTHR23338, PTHR23338, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01423, LSM, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00651, Sm, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF50182, SSF50182, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

Q02260-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKLVNFLKKL RNEQVTIELK NGTTVWGTLQ SVSPQMNAIL TDVKLTLPQP 
        60         70         80         90        100
RLNKLNSNGI AMASLYLTGG QQPTASDNIA SLQYINIRGN TIRQIILPDS 
       110        120        130        140 
LNLDSLLVDQ KQLNSLRRSG QIANDPSKKR RRDFGAPANK RPRRGL
Length:146
Mass (Da):16,275
Last modified:October 1, 1993 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i9929F21EB9218447
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
L04669 Genomic DNA Translation: AAA35055.1
Z72858 Genomic DNA Translation: CAA97076.1
AY692847 Genomic DNA Translation: AAT92866.1
BK006941 Genomic DNA Translation: DAA08167.1

Protein sequence database of the Protein Information Resource

More...PIRi		A47264

NCBI Reference Sequences

More...RefSeqi		NP_011588.3, NM_001181203.3

Genome annotation databases

Ensembl fungal genome annotation project

More...EnsemblFungii		YGR074W_mRNA; YGR074W; YGR074W

Database of genes from NCBI RefSeq genomes

More...GeneIDi		852964

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		sce:YGR074W

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L04669 Genomic DNA Translation: AAA35055.1
Z72858 Genomic DNA Translation: CAA97076.1
AY692847 Genomic DNA Translation: AAT92866.1
BK006941 Genomic DNA Translation: DAA08167.1
PIRiA47264
RefSeqiNP_011588.3, NM_001181203.3

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCMelectron microscopy3.80P/T1-146[»]
5GAMelectron microscopy3.70h1-146[»]
5GANelectron microscopy3.60h/l1-146[»]
5GAOelectron microscopy3.60l1-146[»]
5GM6electron microscopy3.50m1-146[»]
5GMKelectron microscopy3.40m/z1-146[»]
5LJ3electron microscopy3.80h/l1-146[»]
5LJ5electron microscopy3.80h/l1-146[»]
5LQWelectron microscopy5.80h1-146[»]
5MPSelectron microscopy3.85h1-146[»]
5MQ0electron microscopy4.17h/l1-146[»]
5NRLelectron microscopy7.20h/l/t1-146[»]
5WSGelectron microscopy4.00V/m1-146[»]
5Y88electron microscopy3.70f/m1-146[»]
5YLZelectron microscopy3.60f/m1-146[»]
5ZWMelectron microscopy3.40Q/b/m1-146[»]
5ZWNelectron microscopy3.30b1-146[»]
5ZWOelectron microscopy3.90Q/b/m1-146[»]
6BK8electron microscopy3.30h/p1-146[»]
6EXNelectron microscopy3.70h/l1-146[»]
6G90electron microscopy4.00h/t1-146[»]
6J6Gelectron microscopy3.20m/z1-146[»]
6J6Helectron microscopy3.60m/z1-146[»]
6J6Nelectron microscopy3.86m/z1-146[»]
6J6Qelectron microscopy3.70m/z1-146[»]
6N7Pelectron microscopy3.60L1-146[»]
6N7Relectron microscopy3.20L1-146[»]
6N7Xelectron microscopy3.60L1-146[»]
SMRiQ02260
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi33316, 382 interactors
ComplexPortaliCPX-1651, PRP19-associated complex
CPX-23, U1 snRNP
CPX-25, U4/U6.U5 tri-snRNP complex
CPX-26, U2 snRNP
CPX-29, U5 snRNP
CPX-30, AAR2-U5 snRNP
CPX-31, U4 snRNP
CPX-32, U4/U6 snRNP
CPX-43, Sm complex
DIPiDIP-227N
IntActiQ02260, 26 interactors
MINTiQ02260
STRINGi4932.YGR074W

Proteomic databases

MaxQBiQ02260
PaxDbiQ02260
PRIDEiQ02260

Genome annotation databases

EnsemblFungiiYGR074W_mRNA; YGR074W; YGR074W
GeneIDi852964
KEGGisce:YGR074W

Organism-specific databases

EuPathDBiFungiDB:YGR074W
SGDiS000003306, SMD1

Phylogenomic databases

eggNOGiKOG3428, Eukaryota
HOGENOMiCLU_123956_2_0_1
InParanoidiQ02260
OMAiTVSPQMN

Miscellaneous databases

Protein Ontology

More...PROi		PR:Q02260
RNActiQ02260, protein

Family and domain databases

InterProiView protein in InterPro
IPR027141, LSm4/Sm_D1/D3
IPR001163, LSM_dom_euk/arc
IPR010920, LSM_dom_sf
PANTHERiPTHR23338, PTHR23338, 1 hit
PfamiView protein in Pfam
PF01423, LSM, 1 hit
SMARTiView protein in SMART
SM00651, Sm, 1 hit
SUPFAMiSSF50182, SSF50182, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiSMD1_YEAST
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q02260
Secondary accession number(s): D6VUK6
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1993
Last modified: December 2, 2020
This is version 181 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names
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