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Entry version 167 (12 Aug 2020)
Sequence version 2 (21 Sep 2011)
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Protein

Exosome complex component RRP40

Gene

RRP40

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

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and in RNA surveillance pathways, preventing translation of aberrant mRNAs. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. RRP40 as peripheral part of the Exo-9 complex is thought to stabilize the hexameric ring of RNase PH-domain subunits.3 Publications

Miscellaneous

Present with 6050 molecules/cell in log phase SD medium.1 Publication

Caution

According to PubMed:17173052 and PubMed:17174896, only DIS3/RRP44 subunit of the exosome core has exonuclease activity.Curated

<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

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 functionRNA-binding
Biological processrRNA processing

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
YEAST:G3O-33533-MONOMER

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-SCE-429958, mRNA decay by 3' to 5' exoribonuclease
R-SCE-450385, Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA
R-SCE-450513, Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA
R-SCE-6791226, Major pathway of rRNA processing in the nucleolus and cytosol

<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:
Exosome complex component RRP40
Alternative name(s):
Ribosomal RNA-processing protein 40
<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:RRP40
Ordered Locus Names:YOL142W
<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 lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
<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 XV

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
FungiDB:YOL142W

Saccharomyces Genome Database

More...
SGDi
S000005502, RRP40

<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, Exosome, 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_00000974531 – 240Exosome complex component RRP40Add BLAST240

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
Q08285

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

More...
PaxDbi
Q08285

PRoteomics IDEntifications database

More...
PRIDEi
Q08285

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
Q08285

<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 RNA exosome complex. Specifically part of the catalytically inactive RNA exosome core (Exo-9) complex which associates with catalytic subunits DIS3 and RRP6 in cytoplasmic- and nuclear-specific RNA exosome complex forms. Exo-9 is formed by a hexameric ring of RNase PH domain-containing subunits and peripheral S1 domain-containing components CSL4, RRP4 and RRP40 located on the top of the ring structure.

2 Publications

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction%5Fsection">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="https://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated at every <a href="http://www.uniprot.org/help/synchronization">UniProt release</a>.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Hide details

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
34275, 23 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...
ComplexPortali
CPX-599, Nuclear/nucleolar exosome complex, DIS3-RRP6 variant
CPX-603, Cytoplasmic exosome complex, DIS3 variant

Database of interacting proteins

More...
DIPi
DIP-5330N

Protein interaction database and analysis system

More...
IntActi
Q08285, 17 interactors

Molecular INTeraction database

More...
MINTi
Q08285

STRING: functional protein association networks

More...
STRINGi
4932.YOL142W

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...
RNActi
Q08285, 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

1240
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
Q08285

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
Q08285

<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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini67 – 137S1 motifAdd BLAST71

<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 RRP40 family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG1004, Eukaryota

Ensembl GeneTree

More...
GeneTreei
ENSGT00940000153596

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_069847_0_0_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q08285

KEGG Orthology (KO)

More...
KOi
K03681

Identification of Orthologs from Complete Genome Data

More...
OMAi
PLRHKEP

Family and domain databases

Conserved Domains Database

More...
CDDi
cd05790, S1_Rrp40, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.1370.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR026699, Exosome_RNA_bind1/RRP40/RRP4
IPR004088, KH_dom_type_1
IPR036612, KH_dom_type_1_sf
IPR012340, NA-bd_OB-fold
IPR041054, Rrp40_N
IPR037319, Rrp40_S1

The PANTHER Classification System

More...
PANTHERi
PTHR21321, PTHR21321, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF15985, KH_6, 1 hit
PF18311, Rrp40_N, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF50249, SSF50249, 1 hit
SSF54791, SSF54791, 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.

Q08285-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSTFIFPGDS FPVDPTTPVK LGPGIYCDPN TQEIRPVNTG VLHVSAKGKS
60 70 80 90 100
GVQTAYIDYS SKRYIPSVND FVIGVIIGTF SDSYKVSLQN FSSSVSLSYM
110 120 130 140 150
AFPNASKKNR PTLQVGDLVY ARVCTAEKEL EAEIECFDST TGRDAGFGIL
160 170 180 190 200
EDGMIIDVNL NFARQLLFNN DFPLLKVLAA HTKFEVAIGL NGKIWVKCEE
210 220 230 240
LSNTLACYRT IMECCQKNDT AAFKDIAKRQ FKEILTVKEE
Length:240
Mass (Da):26,556
Last modified:September 21, 2011 - v2
<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:i62B3A30348BBAA7C
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 conflicti160L → F in CAA99163 (PubMed:9169874).Curated1

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
Z74884 Genomic DNA Translation: CAA99163.1
AY692926 Genomic DNA Translation: AAT92945.1
BK006948 Genomic DNA Translation: DAA10643.2

Protein sequence database of the Protein Information Resource

More...
PIRi
S61872

NCBI Reference Sequences

More...
RefSeqi
NP_014499.2, NM_001183396.2

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YOL142W_mRNA; YOL142W; YOL142W

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
854023

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YOL142W

<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
Z74884 Genomic DNA Translation: CAA99163.1
AY692926 Genomic DNA Translation: AAT92945.1
BK006948 Genomic DNA Translation: DAA10643.2
PIRiS61872
RefSeqiNP_014499.2, NM_001183396.2

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
2JA9X-ray2.20A62-236[»]
4IFDX-ray2.80G1-240[»]
4OO1X-ray3.30G1-240[»]
5C0WX-ray4.60G1-240[»]
5C0XX-ray3.81G1-240[»]
5G06electron microscopy4.20G1-240[»]
5JEAX-ray2.65G1-240[»]
5K36X-ray3.10G1-240[»]
5OKZX-ray3.20G/Q/a/k1-240[»]
5VZJX-ray3.30G1-240[»]
6FSZelectron microscopy4.60GG1-240[»]
SMRiQ08285
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi34275, 23 interactors
ComplexPortaliCPX-599, Nuclear/nucleolar exosome complex, DIS3-RRP6 variant
CPX-603, Cytoplasmic exosome complex, DIS3 variant
DIPiDIP-5330N
IntActiQ08285, 17 interactors
MINTiQ08285
STRINGi4932.YOL142W

PTM databases

iPTMnetiQ08285

Proteomic databases

MaxQBiQ08285
PaxDbiQ08285
PRIDEiQ08285

Genome annotation databases

EnsemblFungiiYOL142W_mRNA; YOL142W; YOL142W
GeneIDi854023
KEGGisce:YOL142W

Organism-specific databases

EuPathDBiFungiDB:YOL142W
SGDiS000005502, RRP40

Phylogenomic databases

eggNOGiKOG1004, Eukaryota
GeneTreeiENSGT00940000153596
HOGENOMiCLU_069847_0_0_1
InParanoidiQ08285
KOiK03681
OMAiPLRHKEP

Enzyme and pathway databases

BioCyciYEAST:G3O-33533-MONOMER
ReactomeiR-SCE-429958, mRNA decay by 3' to 5' exoribonuclease
R-SCE-450385, Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA
R-SCE-450513, Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA
R-SCE-6791226, Major pathway of rRNA processing in the nucleolus and cytosol

Miscellaneous databases

EvolutionaryTraceiQ08285

Protein Ontology

More...
PROi
PR:Q08285
RNActiQ08285, protein

Family and domain databases

CDDicd05790, S1_Rrp40, 1 hit
Gene3Di3.30.1370.10, 1 hit
InterProiView protein in InterPro
IPR026699, Exosome_RNA_bind1/RRP40/RRP4
IPR004088, KH_dom_type_1
IPR036612, KH_dom_type_1_sf
IPR012340, NA-bd_OB-fold
IPR041054, Rrp40_N
IPR037319, Rrp40_S1
PANTHERiPTHR21321, PTHR21321, 1 hit
PfamiView protein in Pfam
PF15985, KH_6, 1 hit
PF18311, Rrp40_N, 1 hit
SUPFAMiSSF50249, SSF50249, 1 hit
SSF54791, SSF54791, 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 nameiRRP40_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: Q08285
Secondary accession number(s): D6W1S7, E9P8Z4
<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: June 1, 2001
Last sequence update: September 21, 2011
Last modified: August 12, 2020
This is version 167 of the entry and version 2 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, Reference proteome

Documents

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