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Ubiquitin-60S ribosomal protein L40-1



Arabidopsis thaliana (Mouse-ear cress)
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript 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-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 L40-1: component of the 60S subunit of the ribosome.


Ubiquitin is encoded by 16 different genes. Ubiquitin is generally synthesized as a polyubiquitin precursor with tandem head to tail repeats. Often, there is one to three additional amino acids after the last repeat, removed in the mature protein. Alternatively, ubiquitin extension protein is synthesized as a single copy of ubiquitin fused to a ribosomal protein (either L40 or S27A) or to a ubiquitin-related protein (either RUB1 or RUB2). Following translation, extension protein is cleaved from ubiquitin.

GO - Molecular functioni

  • structural constituent of ribosome Source: CAFA

GO - Biological processi

  • mature ribosome assembly Source: CAFA
  • translation Source: InterPro


Molecular functionRibonucleoprotein, Ribosomal protein

Enzyme and pathway databases

ReactomeiR-ATH-110312. Translesion synthesis by REV1.
R-ATH-110314. Recognition of DNA damage by PCNA-containing replication complex.
R-ATH-110320. Translesion Synthesis by POLH.
R-ATH-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-ATH-174184. Cdc20:Phospho-APC/C mediated degradation of Cyclin A.
R-ATH-1799339. SRP-dependent cotranslational protein targeting to membrane.
R-ATH-349425. Autodegradation of the E3 ubiquitin ligase COP1.
R-ATH-382556. ABC-family proteins mediated transport.
R-ATH-446652. Interleukin-1 signaling.
R-ATH-450302. activated TAK1 mediates p38 MAPK activation.
R-ATH-450321. JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1.
R-ATH-532668. N-glycan trimming in the ER and Calnexin/Calreticulin cycle.
R-ATH-5358346. Hedgehog ligand biogenesis.
R-ATH-5632684. Hedgehog 'on' state.
R-ATH-5655862. Translesion synthesis by POLK.
R-ATH-5656121. Translesion synthesis by POLI.
R-ATH-5656169. Termination of translesion DNA synthesis.
R-ATH-5687128. MAPK6/MAPK4 signaling.
R-ATH-5689603. UCH proteinases.
R-ATH-5689877. Josephin domain DUBs.
R-ATH-5689880. Ub-specific processing proteases.
R-ATH-5689901. Metalloprotease DUBs.
R-ATH-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-ATH-5696394. DNA Damage Recognition in GG-NER.
R-ATH-5696395. Formation of Incision Complex in GG-NER.
R-ATH-5696397. Gap-filling DNA repair synthesis and ligation in GG-NER.
R-ATH-5696400. Dual Incision in GG-NER.
R-ATH-6781823. Formation of TC-NER Pre-Incision Complex.
R-ATH-6782135. Dual incision in TC-NER.
R-ATH-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-ATH-68949. Orc1 removal from chromatin.
R-ATH-69017. CDK-mediated phosphorylation and removal of Cdc6.
R-ATH-69229. Ubiquitin-dependent degradation of Cyclin D1.
R-ATH-69231. Cyclin D associated events in G1.
R-ATH-72689. Formation of a pool of free 40S subunits.
R-ATH-72706. GTP hydrolysis and joining of the 60S ribosomal subunit.
R-ATH-8854050. FBXL7 down-regulates AURKA during mitotic entry and in early mitosis.
R-ATH-8866652. Synthesis of active ubiquitin: roles of E1 and E2 enzymes.
R-ATH-8866654. E3 ubiquitin ligases ubiquitinate target proteins.
R-ATH-901032. ER Quality Control Compartment (ERQC).
R-ATH-917729. Endosomal Sorting Complex Required For Transport (ESCRT).
R-ATH-917937. Iron uptake and transport.
R-ATH-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-ATH-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
R-ATH-983168. Antigen processing: Ubiquitination & Proteasome degradation.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-60S ribosomal protein L40-1
Cleaved into the following 2 chains:
Alternative name(s):
Gene namesi
Ordered Locus Names:At2g36170
ORF Names:F9C22.10
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRilocus:2053496. AT2G36170.

Subcellular locationi

Ubiquitin :

GO - Cellular componenti

  • cytosolic large ribosomal subunit Source: TAIR
  • nucleolus Source: TAIR

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003968651 – 76UbiquitinAdd BLAST76
ChainiPRO_000013875877 – 12860S ribosomal protein L40-1Add BLAST52

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)PROSITE-ProRule annotation

Keywords - PTMi

Isopeptide bond

Proteomic databases


PTM databases



Gene expression databases

ExpressionAtlasiB9DHA6. baseline and differential.
GenevisibleiB9DHA6. AT.


Subunit structurei

Ribosomal protein L40-1 is part of the 60S ribosomal subunit.By similarity

Protein-protein interaction databases

BioGridi3533. 1 interactor.
9743. 12 interactors.


3D structure databases


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

eggNOGiENOG410IUNU. Eukaryota.
COG1552. LUCA.

Family and domain databases

InterProiView protein in InterPro
IPR001975. Ribosomal_L40e.
IPR011332. Ribosomal_zn-bd.
IPR019956. Ubiquitin.
IPR029071. Ubiquitin-rel_dom.
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.
SSF57829. SSF57829. 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.

B9DHA6-1 [UniParc]FASTAAdd to basket

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60 70 80 90 100
110 120
Mass (Da):14,733
Last modified:March 24, 2009 - v1

Sequence databases

Select the link destinations:
Links Updated
J05508 Genomic DNA. Translation: AAA32905.1.
AC006921 Genomic DNA. No translation available.
AC007135 Genomic DNA. Translation: AAM15407.1.
CP002685 Genomic DNA. Translation: AEC09212.1.
AF360311 mRNA. Translation: AAK26021.1.
AY056360 mRNA. Translation: AAL07246.1.
AK317456 mRNA. Translation: BAH20123.1.
RefSeqiNP_565836.1. NM_129175.3.
NP_566969.1. NM_115119.4.

Genome annotation databases

EnsemblPlantsiAT2G36170.1; AT2G36170.1; AT2G36170.
AT3G52590.1; AT3G52590.1; AT3G52590.
GrameneiAT2G36170.1; AT2G36170.1; AT2G36170.
AT3G52590.1; AT3G52590.1; AT3G52590.

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.

Entry informationi

Entry nameiRL40A_ARATH
AccessioniPrimary (citable) accession number: B9DHA6
Secondary accession number(s): O80715
, P19232, P59263, Q38875, Q9LDJ2, Q9LYW1, Q9M0W3, Q9M1P9, Q9S7X3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 10, 2010
Last sequence update: March 24, 2009
Last modified: June 7, 2017
This is version 68 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program


Keywords - Technical termi

Complete proteome, Reference proteome


  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. Ribosomal proteins
    Ribosomal proteins families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families