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Ubiquitin-60S ribosomal protein L40



Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Reviewed-Annotation score: -Experimental evidence at protein leveli


Ubiquitin: Exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).By similarity
60S ribosomal protein L40-B: Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded message by selecting cognate aminoacyl-transfer RNA (tRNA) molecules. The large subunit (LSU) contains the ribosomal catalytic site termed the peptidyl transferase center (PTC), which catalyzes the formation of peptide bonds, thereby polymerizing the amino acids delivered by tRNAs into a polypeptide chain. The nascent polypeptides leave the ribosome through a tunnel in the LSU and interact with protein factors that function in enzymatic processing, targeting, and the membrane insertion of nascent chains at the exit of the ribosomal tunnel (PubMed:22096102). eL40 is essential for translation of a subset of cellular transcripts, including stress response transcripts, such as DDR2 (PubMed:23169626).1 Publication1 Publication


Ubiquitin is encoded by several different genes. UBI1 and UBI2 genes code for a single copy of ubiquitin fused to the ribosomal proteins eL40. UBI3 is a polyprotein with one copy of ubiquitin fused to ribosomal protein eS31. UBI4 is a polyprotein containing 5 exact head to tail repeats of ubiquitin.1 Publication
The 60S ribosomal protein L40 is present with 40000 molecules/cell in log phase SD medium.1 Publication

GO - Molecular functioni

  • protein tag Source: SGD
  • structural constituent of ribosome Source: SGD

GO - Biological processi

  • cytoplasmic translation Source: SGD
  • protein ubiquitination Source: SGD
  • ribosomal large subunit assembly Source: SGD
  • ribosomal large subunit export from nucleus Source: SGD
  • ribosome biogenesis Source: SGD


Molecular functionRibonucleoprotein, Ribosomal protein

Enzyme and pathway databases

ReactomeiR-SCE-110312. Translesion synthesis by REV1.
R-SCE-110314. Recognition of DNA damage by PCNA-containing replication complex.
R-SCE-110320. Translesion Synthesis by POLH.
R-SCE-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-SCE-174113. SCF-beta-TrCP mediated degradation of Emi1.
R-SCE-1799339. SRP-dependent cotranslational protein targeting to membrane.
R-SCE-349425. Autodegradation of the E3 ubiquitin ligase COP1.
R-SCE-382556. ABC-family proteins mediated transport.
R-SCE-450408. AUF1 (hnRNP D0) binds and destabilizes mRNA.
R-SCE-5655862. Translesion synthesis by POLK.
R-SCE-5656121. Translesion synthesis by POLI.
R-SCE-5656169. Termination of translesion DNA synthesis.
R-SCE-5675221. Negative regulation of MAPK pathway.
R-SCE-5687128. MAPK6/MAPK4 signaling.
R-SCE-5689603. UCH proteinases.
R-SCE-5689880. Ub-specific processing proteases.
R-SCE-5689901. Metalloprotease DUBs.
R-SCE-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-SCE-5696394. DNA Damage Recognition in GG-NER.
R-SCE-5696395. Formation of Incision Complex in GG-NER.
R-SCE-5696397. Gap-filling DNA repair synthesis and ligation in GG-NER.
R-SCE-5696400. Dual Incision in GG-NER.
R-SCE-6781823. Formation of TC-NER Pre-Incision Complex.
R-SCE-6782135. Dual incision in TC-NER.
R-SCE-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SCE-68949. Orc1 removal from chromatin.
R-SCE-69017. CDK-mediated phosphorylation and removal of Cdc6.
R-SCE-69229. Ubiquitin-dependent degradation of Cyclin D1.
R-SCE-69601. Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
R-SCE-72689. Formation of a pool of free 40S subunits.
R-SCE-72706. GTP hydrolysis and joining of the 60S ribosomal subunit.
R-SCE-8854050. FBXL7 down-regulates AURKA during mitotic entry and in early mitosis.
R-SCE-8866652. Synthesis of active ubiquitin: roles of E1 and E2 enzymes.
R-SCE-8866654. E3 ubiquitin ligases ubiquitinate target proteins.
R-SCE-917937. Iron uptake and transport.
R-SCE-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-SCE-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
R-SCE-983168. Antigen processing: Ubiquitination & Proteasome degradation.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-60S ribosomal protein L40
Cleaved into the following 2 chains:
60S ribosomal protein L40-B1 Publication
Alternative name(s):
Large ribosomal subunit protein eL40-B1 Publication
Gene namesi
Name:RPL40B1 Publication
Ordered Locus Names:YKR094C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
  • UP000002311 Componenti: Chromosome XI

Organism-specific databases

SGDiS000001802. RPL40B.

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; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi


Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi29K → R: Deficiency in ubiquitin-protein conjugate formation. 1 Publication1
Mutagenesisi48K → R: Deficiency in ubiquitin-protein conjugate formation. 1 Publication1
Mutagenesisi63K → R: Deficiency in ubiquitin-protein conjugate formation. Loss of DNA repair function. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003964551 – 76UbiquitinAdd BLAST76
ChainiPRO_000039645677 – 12860S ribosomal protein L40-BAdd BLAST52

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
Cross-linki93Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases


2D gel databases


PTM databases



Gene expression databases

ExpressionAtlasiP0CH09. differential.


Subunit structurei

Component of the large ribosomal subunit (LSU). Mature yeast ribosomes consist of a small (40S) and a large (60S) subunit. The 40S small subunit contains 1 molecule of ribosomal RNA (18S rRNA) and 33 different proteins (encoded by 57 genes). The large 60S subunit contains 3 rRNA molecules (25S, 5.8S and 5S rRNA) and 46 different proteins (encoded by 81 genes) (PubMed:9559554, PubMed:22096102).1 Publication1 Publication

Protein-protein interaction databases

BioGridi34225. 357 interactors.
34844. 178 interactors.


3D structure databases

Select the link destinations:
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4V91electron microscopy3.70m1-128[»]

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 76Ubiquitin-likePROSITE-ProRule annotationAdd BLAST76

Sequence similaritiesi

In the N-terminal section; belongs to the ubiquitin family.Curated
In the C-terminal section; belongs to the eukaryotic ribosomal protein eL40 family.Curated

Phylogenomic databases


Family and domain databases

Gene3Di2.20.28.70. 1 hit.
InterProiView protein in InterPro
IPR038587. L40e_sf.
IPR001975. Ribosomal_L40e.
IPR019956. Ubiquitin.
IPR029071. Ubiquitin-like_domsf.
IPR019954. Ubiquitin_CS.
IPR000626. Ubiquitin_dom.
PfamiView protein in Pfam
PF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
SMARTiView protein in SMART
SM01377. Ribosomal_L40e. 1 hit.
SM00213. UBQ. 1 hit.
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiView protein in PROSITE
PS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.


Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0CH09-1 [UniParc]FASTAAdd to basket

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60 70 80 90 100
110 120
Mass (Da):14,554
Last modified:August 10, 2010 - v1

Sequence databases

Select the link destinations:
Links Updated
X73541 Genomic DNA. Translation: CAA51949.1.
Z28319 Genomic DNA. Translation: CAA82173.1.
BK006944 Genomic DNA. Translation: DAA09244.1.
RefSeqiNP_012118.1. NM_001179496.1.
NP_013020.3. NM_001179884.3.

Genome annotation databases

EnsemblFungiiYIL148W; YIL148W; YIL148W.
YKR094C; YKR094C; YKR094C.

Similar proteinsi

Entry informationi

Entry nameiRL40B_YEAST
AccessioniPrimary (citable) accession number: P0CH09
Secondary accession number(s): D6VVD9
, P04838, P14796, P61864, Q6LA96
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 10, 2010
Last sequence update: August 10, 2010
Last modified: March 28, 2018
This is version 72 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program


Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome