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Entry version 159 (03 Jul 2019)
Sequence version 1 (01 Nov 1995)
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Protein

Small nuclear ribonucleoprotein Sm D3

Gene

SMD3

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

<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

GO - Biological processi

<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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
YEAST:G3O-32283-MONOMER

<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_and_taxonomy_section">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 D3
Short name:
Sm-D3
Alternative name(s):
snRNP core protein D3
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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:SMD3
Ordered Locus Names:YLR147C
ORF Names:L9634.6
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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_and_taxonomy_section">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_and_taxonomy_section">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 lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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_manual">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 XII

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
FungiDB:YLR147C

Saccharomyces Genome Database

More...
SGDi
S000004137 SMD3

<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

Cytoplasm, 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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001222201 – 101Small nuclear ribonucleoprotein Sm D3Add BLAST101

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
P43321

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

More...
PaxDbi
P43321

PRoteomics IDEntifications database

More...
PRIDEi
P43321

Consortium for Top Down Proteomics

More...
TopDownProteomicsi
P43321

<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_section">'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_section">'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. SMD3 specifically interacts with SMB1. 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.

4 Publications

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

WithEntry#Exp.IntActNotes
SMB1P400183EBI-529,EBI-432

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
31416, 69 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-715N

Protein interaction database and analysis system

More...
IntActi
P43321, 26 interactors

Molecular INTeraction database

More...
MINTi
P43321

STRING: functional protein association networks

More...
STRINGi
4932.YLR147C

<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

1101
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

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SMRi
P43321

Database of comparative protein structure models

More...
ModBasei
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

<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

Ensembl GeneTree

More...
GeneTreei
ENSGT00610000086153

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000182712

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P43321

KEGG Orthology (KO)

More...
KOi
K11088

Identification of Orthologs from Complete Genome Data

More...
OMAi
IMRANAR

Family and domain databases

Conserved Domains Database

More...
CDDi
cd01721 Sm_D3, 1 hit

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
IPR034099 SmD3

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_length">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_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">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.

P43321-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTMNGIPVKL LNEAQGHIVS LELTTGATYR GKLVESEDSM NVQLRDVIAT
60 70 80 90 100
EPQGAVTHMD QIFVRGSQIK FIVVPDLLKN APLFKKNSSR PMPPIRGPKR

R
Length:101
Mass (Da):11,224
Last modified:November 1, 1995 - 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:iBB02A56C5AD70CF2
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti88S → P in AAS56859 (PubMed:17322287).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
M65144 Genomic DNA No translation available.
Z73319 Genomic DNA Translation: CAA97719.1
U53879 Genomic DNA Translation: AAB82381.1
AY558533 Genomic DNA Translation: AAS56859.1
BK006945 Genomic DNA Translation: DAA09458.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S29093

NCBI Reference Sequences

More...
RefSeqi
NP_013248.1, NM_001182034.1

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YLR147C_mRNA; YLR147C_mRNA; YLR147C

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
850839

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YLR147C

<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
M65144 Genomic DNA No translation available.
Z73319 Genomic DNA Translation: CAA97719.1
U53879 Genomic DNA Translation: AAB82381.1
AY558533 Genomic DNA Translation: AAS56859.1
BK006945 Genomic DNA Translation: DAA09458.1
PIRiS29093
RefSeqiNP_013248.1, NM_001182034.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

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RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCMelectron microscopy3.80J/R1-101[»]
5GAMelectron microscopy3.70d1-101[»]
5GANelectron microscopy3.60d/n1-101[»]
5GAOelectron microscopy3.60n1-101[»]
5GM6electron microscopy3.50l1-101[»]
5GMKelectron microscopy3.40l/y1-101[»]
5LJ3electron microscopy3.80d/n1-101[»]
5LJ5electron microscopy3.80d/n1-101[»]
5LQWelectron microscopy5.80d1-101[»]
5MPSelectron microscopy3.85d1-101[»]
5MQ0electron microscopy4.17d/n1-101[»]
5NRLelectron microscopy7.20d/n/v1-101[»]
5UZ5electron microscopy3.56N1-101[»]
5WSGelectron microscopy4.00U/l1-101[»]
5Y88electron microscopy3.70e/l1-101[»]
5YLZelectron microscopy3.60e/l1-101[»]
5ZWMelectron microscopy3.40S/d/l1-101[»]
5ZWNelectron microscopy3.30d1-101[»]
5ZWOelectron microscopy3.90S/d/l1-101[»]
6BK8electron microscopy3.30g/o1-101[»]
6EXNelectron microscopy3.70d/n1-101[»]
6G90electron microscopy4.00d/v1-101[»]
6J6Gelectron microscopy3.20l/y1-101[»]
6J6Helectron microscopy3.60l/y1-101[»]
6J6Nelectron microscopy3.86l/y1-101[»]
6J6Qelectron microscopy3.70l/y1-101[»]
SMRiP43321
ModBaseiSearch...

Protein-protein interaction databases

BioGridi31416, 69 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-715N
IntActiP43321, 26 interactors
MINTiP43321
STRINGi4932.YLR147C

Proteomic databases

MaxQBiP43321
PaxDbiP43321
PRIDEiP43321
TopDownProteomicsiP43321

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR147C_mRNA; YLR147C_mRNA; YLR147C
GeneIDi850839
KEGGisce:YLR147C

Organism-specific databases

EuPathDBiFungiDB:YLR147C
SGDiS000004137 SMD3

Phylogenomic databases

GeneTreeiENSGT00610000086153
HOGENOMiHOG000182712
InParanoidiP43321
KOiK11088
OMAiIMRANAR

Enzyme and pathway databases

BioCyciYEAST:G3O-32283-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P43321

Family and domain databases

CDDicd01721 Sm_D3, 1 hit
InterProiView protein in InterPro
IPR027141 LSm4/Sm_D1/D3
IPR001163 LSM_dom_euk/arc
IPR010920 LSM_dom_sf
IPR034099 SmD3
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 nameiSMD3_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: P43321
Secondary accession number(s): D6VYE2, E9P8W3
<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_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: July 3, 2019
This is version 159 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, Complete proteome, 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 chromosome XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
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