Protein Help

RPT4 / YOR259C 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
CRL13 8 , PCS1 , SUG2 8
Protein Product
proteasome regulatory particle base subunit RPT4
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.


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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-life11.2 hrChristiano R, et al. (2014)

Protein Abundance

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Abundance (molecules/cell)MediaTreatmentTreatment timeFold ChangeVisualizationStrain backgroundOriginal ReferenceReference
1138SDuntreatedconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
10042SDuntreatedconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
9850SD0.2 M hydroxyurea160 minconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
8285SD200 ng/ml sirolimus700 minconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
2988YEPDuntreatedflow cytometry evidenceS288CDavidson GS, et al. (2011)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.


rpt4-(sug2-13) | rpt4-145 | rpt4-150 | rpt4-EQ | rpt4-Δ | rpt4R

View all RPT4 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 MSEEQDPLLA GLGETSGDNH TQQSHEQQPE QPQETEEHHE EEPSRVDPEQ EAHNKALNQF
61 KRKLLEHRRY DDQLKQRRQN IRDLEKLYDK TENDIKALQS IGQLIGEVMK ELSEEKYIVK
121 ASSGPRYIVG VRNSVDRSKL KKGVRVTLDI TTLTIMRILP RETDPLVYNM TSFEQGEITF
181 DGIGGLTEQI RELREVIELP LKNPEIFQRV GIKPPKGVLL YGPPGTGKTL LAKAVAATIG
241 ANFIFSPASG IVDKYIGESA RIIREMFAYA KEHEPCIIFM DEVDAIGGRR FSEGTSADRE
301 IQRTLMELLT QMDGFDNLGQ TKIIMATNRP DTLDPALLRP GRLDRKVEIP LPNEAGRLEI
361 FKIHTAKVKK TGEFDFEAAV KMSDGFNGAD IRNCATEAGF FAIRDDRDHI NPDDLMKAVR
421 KVAEVKKLEG TIEYQKL*

* 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.

11 entries for 7 sites

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SiteModificationModifierReference
K75ubiquitinylated lysineSwaney DL, et al. (2013) PMID: 23749301
T187phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S292phosphorylated residueAlbuquerque CP, et al. (2008) PMID: 18407956
S292phosphorylated residueMacGilvray ME, et al. (2020) PMID: 32597660
S292phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S292phosphorylated residueZhou X, et al. (2021) PMID: 33481703
S292phosphorylated residueKikuchi J, et al. (2010) PMID: 20486117
S296phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
K362monoacetylated residueHenriksen P, et al. (2012) PMID: 22865919
K370monoacetylated residueŠoštarić N, et al. (2018) PMID: 30181345
Showing 1 to 10 of 11 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
A286.41
C20.46
D296.64
E4510.30
F163.66
G327.32
H92.06
I347.78
K327.32
L388.70
M112.52
N153.43
P225.03
Q214.81
R317.09
S173.89
T255.72
V214.81
W00.00
Y92.06

Physical Details

Length (a.a): 437
Molecular Weight (Da): 49397.7
Isoelectric Point (pl): 5.45
Formula: C2170H3493N616O673S13
Aliphatic Index: 80.57
Instability Index: 40.11

Coding Region Translation Calculations

Codon Bias: 0.23
Codon Adaptation Index: 0.21
Frequence of Optimal Codons: 0.56
Hydropathicity of Protein: -0.6
Aromaticity Score: 0.06

Extinction Coefficients at 280nm

ALL Cys residues appear as half cystines: 13535.0
NO Cys residues appear as half cystines: 13410.0

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 11 sources


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External IDSource
AN5747AspGD
orf19.482CGD
1589DIP
AAB51594.1GenBank/EMBL/DDBJ
AAA85134.1GenBank/EMBL/DDBJ
CAA99481.1GenBank/EMBL/DDBJ
Z75167GenBank/EMBL/DDBJ
U43720GenBank/EMBL/DDBJ
U93262GenBank/EMBL/DDBJ
398365977GenBank/EMBL/DDBJ
Showing 1 to 10 of 31 entries

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