Protein Help

RRP40 / YOL142W Protein

Protein abundance data, domains, shared domains with other proteins, protein sequence retrieval for various strains, sequence-based physico-chemical properties, protein modification sites, and external identifiers for the protein.


Aliases
MTR14 19
Protein Product
exosome non-catalytic core subunit RRP40
Feature Type
ORF , Verified

AlphaFold Protein Structure

AlphaFold, developed by DeepMind, is an AI program that accurately predicts protein structures from amino acid sequences, enabling visualization of protein conformations. The predicted structures can be accessed through the Protein Data Bank (PDB) and AlphaFold Protein Structure Database.


Model Confidence

Very high
Confident
Low
Very low

Experimental Data

Contains experimentally-derived protein half-life data obtained using stable isotope labeling by amino acids (SILAC) coupled with mass spectrometry. This section also contains protein abundance data for both untreated and treated cells obtained from over 20 studies. These data have been normalized and converted to a common unit of molecules per cell.


Protein Half Life

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ExperimentResultReference
half-life9.5 hrChristiano R, et al. (2014)

Protein Abundance

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Abundance (molecules/cell)MediaTreatmentTreatment timeFold ChangeVisualizationStrain backgroundOriginal ReferenceReference
6009SDuntreatedconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
4811SD2 mM 1,4-dithiothreitol2 hrconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
3738SD1 mM hydrogen peroxide1 hr0.62confocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
4218SD minus nitrogencellular response to nitrogen starvation15 hrconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
4832SDuntreatedconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
Showing 1 to 5 of 26 entries

Domains and Classification - S288C

Collection of computationally identified domains and motifs, as determined by InterProScan analysis; includes protein coordinates for the domain, a domain Description, a Source and corresponding accession ID, and the number of S. cerevisiae genes that share the same domain.


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Gene Protein Coordinates Accession ID Description Source No. of Genes with Domain

Domain Locations

Visual representation of the locations of the domains within the protein, as listed in the Domains and Classification table. Each row displays the domain(s) derived from a different Source, with domains color-coded according to this Source.

Scroll over a domain to view its exact coordinates and its Description.

Shared Domains

This diagram displays domains (colored squares) shared between the given protein (yellow circle) and other proteins (gray circles); the domains are color-coded according to their source, as displayed in the Domain Locations table, above.

Reset

Click on a gene or domain name to go to its specific page within SGD; drag any of the gene or domain objects around within the visualization for easier viewing; click “Reset” to automatically redraw the diagram.

Alleles

Curated mutant alleles for the specified gene, listed alphabetically. Click on the allele name to open the allele page. Click "SGD search" to view all alleles in search results.


rrp40-G8A | rrp40-S87A | rrp40-W195R | rrp40-Δ

View all RRP40 alleles in SGD search

Sequence

Protein sequence for the given gene in S288C and other strains, when available. Use the pull-down menu under "Strain" to select the sequence for a specific strain. The displayed sequence can be downloaded in FASTA format as a .txt file. Amino acids displayed in blue represent modification sites. More detailed evidence for these modification sites is presented in the Post-translational Modifications table, located just below the protein sequence.


1 MSTFIFPGDS FPVDPTTPVK LGPGIYCDPN TQEIRPVNTG VLHVSAKGKS GVQTAYIDYS
61 SKRYIPSVND FVIGVIIGTF SDSYKVSLQN FSSSVSLSYM AFPNASKKNR PTLQVGDLVY
121 ARVCTAEKEL EAEIECFDST TGRDAGFGIL EDGMIIDVNL NFARQLLFNN DFPLLKVLAA
181 HTKFEVAIGL NGKIWVKCEE LSNTLACYRT IMECCQKNDT AAFKDIAKRQ FKEILTVKEE
241 *

* Blue amino acids indicate modification sites. More information below.

Post-translational Modifications - S288C

Modification sites for the protein in the selected strain, based on the presence of a residue in the specific strain, as inferred from experimental evidence.

7 entries for 7 sites

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SiteModificationModifierReference
T16phosphorylated residueAlbuquerque CP, et al. (2008) PMID: 18407956
T17phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
K49monoacetylated residueŠoštarić N, et al. (2018) PMID: 30181345
K62monoacetylated residueŠoštarić N, et al. (2018) PMID: 30181345
K224monoacetylated residueŠoštarić N, et al. (2018) PMID: 30181345
K232monoacetylated residueŠoštarić N, et al. (2018) PMID: 30181345
K238sumoylated lysineBhagwat NR, et al. (2021) PMID: 33502312
Showing 1 to 7 of 7 entries

Sequence-Based Physico-chemical Properties - S288C

Calculated protein properties, including amino acid composition, length, coding region calculations, and atomic composition.

Amino Acid Composition

Sort table using the arrow to the right of a column header to sort by that column; download all properties as a .txt file using the "Download Properties" button.

Amino AcidFrequencyPercentage
A166.67
C72.92
D145.83
E145.83
F156.25
G156.25
H20.83
I177.08
K177.08
L187.50
M41.67
N135.42
P114.58
Q72.92
R83.33
S187.50
T166.67
V197.92
W10.42
Y83.33

Physical Details

Length (a.a): 240
Molecular Weight (Da): 26553.6
Isoelectric Point (pl): 5.39
Formula: C1190H1863N306O359S11
Aliphatic Index: 83.02
Instability Index: 38.99

Coding Region Translation Calculations

Codon Bias: 0.09
Codon Adaptation Index: 0.14
Frequence of Optimal Codons: 0.49
Hydropathicity of Protein: -0.07
Aromaticity Score: 0.1

Extinction Coefficients at 280nm

ALL Cys residues appear as half cystines: 17795.0
NO Cys residues appear as half cystines: 17420.0

Atomic Composition

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Atom Frequency Percentage

Data not found or not available for  S288C

External Identifiers

List of external identifiers for the protein from various database sources.

31 entries for 10 sources


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External IDSource
orf19.3304CGD
5330DIP
AAT92945.1GenBank/EMBL/DDBJ
CAA99163.1GenBank/EMBL/DDBJ
448262639GenBank/EMBL/DDBJ
Z74884GenBank/EMBL/DDBJ
AY692926GenBank/EMBL/DDBJ
14285754GenBank/EMBL/DDBJ
330443719GenBank/EMBL/DDBJ
122920873GenBank/EMBL/DDBJ
Showing 1 to 10 of 31 entries

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