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Protein

Ubiquitin-60S ribosomal protein L40

Gene

UBA52

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. 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.
60S ribosomal protein L40: Component of the 60S subunit of the ribosome. Ribosomal protein L40 is essential for translation of a subset of cellular transcripts, and especially for cap-dependent translation of vesicular stomatitis virus mRNAs.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei54Activating enzyme1
Sitei68Essential for function1
Binding sitei72Activating enzyme1

GO - Molecular functioni

  • structural constituent of ribosome Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Enzyme and pathway databases

BioCyciZFISH:G66-32465-MONOMER.
ReactomeiR-HSA-110312. Translesion synthesis by REV1.
R-HSA-110314. Recognition of DNA damage by PCNA-containing replication complex.
R-HSA-110320. Translesion Synthesis by POLH.
R-HSA-1169091. Activation of NF-kappaB in B cells.
R-HSA-1169408. ISG15 antiviral mechanism.
R-HSA-1234176. Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha.
R-HSA-1236382. Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants.
R-HSA-1236974. ER-Phagosome pathway.
R-HSA-1253288. Downregulation of ERBB4 signaling.
R-HSA-1295596. Spry regulation of FGF signaling.
R-HSA-1358803. Downregulation of ERBB2:ERBB3 signaling.
R-HSA-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-HSA-156902. Peptide chain elongation.
R-HSA-162588. Budding and maturation of HIV virion.
R-HSA-168638. NOD1/2 Signaling Pathway.
R-HSA-168928. RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways.
R-HSA-174048. APC/C:Cdc20 mediated degradation of Cyclin B.
R-HSA-174084. Autodegradation of Cdh1 by Cdh1:APC/C.
R-HSA-174113. SCF-beta-TrCP mediated degradation of Emi1.
R-HSA-174154. APC/C:Cdc20 mediated degradation of Securin.
R-HSA-174178. APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1.
R-HSA-174184. Cdc20:Phospho-APC/C mediated degradation of Cyclin A.
R-HSA-174490. Membrane binding and targetting of GAG proteins.
R-HSA-175474. Assembly Of The HIV Virion.
R-HSA-179409. APC-Cdc20 mediated degradation of Nek2A.
R-HSA-1799339. SRP-dependent cotranslational protein targeting to membrane.
R-HSA-180534. Vpu mediated degradation of CD4.
R-HSA-180585. Vif-mediated degradation of APOBEC3G.
R-HSA-182971. EGFR downregulation.
R-HSA-187577. SCF(Skp2)-mediated degradation of p27/p21.
R-HSA-192823. Viral mRNA Translation.
R-HSA-195253. Degradation of beta-catenin by the destruction complex.
R-HSA-201681. TCF dependent signaling in response to WNT.
R-HSA-202424. Downstream TCR signaling.
R-HSA-205043. NRIF signals cell death from the nucleus.
R-HSA-209543. p75NTR recruits signalling complexes.
R-HSA-209560. NF-kB is activated and signals survival.
R-HSA-211733. Regulation of activated PAK-2p34 by proteasome mediated degradation.
R-HSA-2122947. NOTCH1 Intracellular Domain Regulates Transcription.
R-HSA-2122948. Activated NOTCH1 Transmits Signal to the Nucleus.
R-HSA-2173788. Downregulation of TGF-beta receptor signaling.
R-HSA-2173791. TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition).
R-HSA-2173795. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
R-HSA-2173796. SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription.
R-HSA-2408557. Selenocysteine synthesis.
R-HSA-2467813. Separation of Sister Chromatids.
R-HSA-2559580. Oxidative Stress Induced Senescence.
R-HSA-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-HSA-2559585. Oncogene Induced Senescence.
R-HSA-2565942. Regulation of PLK1 Activity at G2/M Transition.
R-HSA-2644606. Constitutive Signaling by NOTCH1 PEST Domain Mutants.
R-HSA-2672351. Stimuli-sensing channels.
R-HSA-2691232. Constitutive Signaling by NOTCH1 HD Domain Mutants.
R-HSA-2871837. FCERI mediated NF-kB activation.
R-HSA-2894862. Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants.
R-HSA-2979096. NOTCH2 Activation and Transmission of Signal to the Nucleus.
R-HSA-3134975. Regulation of innate immune responses to cytosolic DNA.
R-HSA-3322077. Glycogen synthesis.
R-HSA-349425. Autodegradation of the E3 ubiquitin ligase COP1.
R-HSA-3769402. Deactivation of the beta-catenin transactivating complex.
R-HSA-3785653. Myoclonic epilepsy of Lafora.
R-HSA-382556. ABC-family proteins mediated transport.
R-HSA-400253. Circadian Clock.
R-HSA-445989. TAK1 activates NFkB by phosphorylation and activation of IKKs complex.
R-HSA-446652. Interleukin-1 signaling.
R-HSA-450302. activated TAK1 mediates p38 MAPK activation.
R-HSA-450321. JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1.
R-HSA-450408. AUF1 (hnRNP D0) binds and destabilizes mRNA.
R-HSA-4608870. Asymmetric localization of PCP proteins.
R-HSA-4641257. Degradation of AXIN.
R-HSA-4641258. Degradation of DVL.
R-HSA-4641263. Regulation of FZD by ubiquitination.
R-HSA-5205685. Pink/Parkin Mediated Mitophagy.
R-HSA-532668. N-glycan trimming in the ER and Calnexin/Calreticulin cycle.
R-HSA-5357905. Regulation of TNFR1 signaling.
R-HSA-5357956. TNFR1-induced NFkappaB signaling pathway.
R-HSA-5358346. Hedgehog ligand biogenesis.
R-HSA-5362768. Hh mutants that don't undergo autocatalytic processing are degraded by ERAD.
R-HSA-5607761. Dectin-1 mediated noncanonical NF-kB signaling.
R-HSA-5607764. CLEC7A (Dectin-1) signaling.
R-HSA-5610780. Degradation of GLI1 by the proteasome.
R-HSA-5610783. Degradation of GLI2 by the proteasome.
R-HSA-5610785. GLI3 is processed to GLI3R by the proteasome.
R-HSA-5632684. Hedgehog 'on' state.
R-HSA-5654726. Negative regulation of FGFR1 signaling.
R-HSA-5654727. Negative regulation of FGFR2 signaling.
R-HSA-5654732. Negative regulation of FGFR3 signaling.
R-HSA-5654733. Negative regulation of FGFR4 signaling.
R-HSA-5655862. Translesion synthesis by POLK.
R-HSA-5656121. Translesion synthesis by POLI.
R-HSA-5656169. Termination of translesion DNA synthesis.
R-HSA-5658442. Regulation of RAS by GAPs.
R-HSA-5668541. TNFR2 non-canonical NF-kB pathway.
R-HSA-5675221. Negative regulation of MAPK pathway.
R-HSA-5675482. Regulation of necroptotic cell death.
R-HSA-5676590. NIK-->noncanonical NF-kB signaling.
R-HSA-5678895. Defective CFTR causes cystic fibrosis.
R-HSA-5684264. MAP3K8 (TPL2)-dependent MAPK1/3 activation.
R-HSA-5685942. HDR through Homologous Recombination (HRR).
R-HSA-5687128. MAPK6/MAPK4 signaling.
R-HSA-5689603. UCH proteinases.
R-HSA-5689877. Josephin domain DUBs.
R-HSA-5689880. Ub-specific processing proteases.
R-HSA-5689896. Ovarian tumor domain proteases.
R-HSA-5689901. Metalloprotease DUBs.
R-HSA-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-HSA-5693607. Processing of DNA double-strand break ends.
R-HSA-5696394. DNA Damage Recognition in GG-NER.
R-HSA-5696395. Formation of Incision Complex in GG-NER.
R-HSA-5696397. Gap-filling DNA repair synthesis and ligation in GG-NER.
R-HSA-5696400. Dual Incision in GG-NER.
R-HSA-6781823. Formation of TC-NER Pre-Incision Complex.
R-HSA-6781827. Transcription-Coupled Nucleotide Excision Repair (TC-NER).
R-HSA-6782135. Dual incision in TC-NER.
R-HSA-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-HSA-6783310. Fanconi Anemia Pathway.
R-HSA-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.
R-HSA-6804756. Regulation of TP53 Activity through Phosphorylation.
R-HSA-6804757. Regulation of TP53 Degradation.
R-HSA-6804760. Regulation of TP53 Activity through Methylation.
R-HSA-6807004. Negative regulation of MET activity.
R-HSA-68827. CDT1 association with the CDC6:ORC:origin complex.
R-HSA-68949. Orc1 removal from chromatin.
R-HSA-69017. CDK-mediated phosphorylation and removal of Cdc6.
R-HSA-69229. Ubiquitin-dependent degradation of Cyclin D1.
R-HSA-69231. Cyclin D associated events in G1.
R-HSA-69298. Association of licensing factors with the pre-replicative complex.
R-HSA-69481. G2/M Checkpoints.
R-HSA-69541. Stabilization of p53.
R-HSA-69601. Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
R-HSA-72689. Formation of a pool of free 40S subunits.
R-HSA-72706. GTP hydrolysis and joining of the 60S ribosomal subunit.
R-HSA-72764. Eukaryotic Translation Termination.
R-HSA-8849469. PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1.
R-HSA-8852276. The role of GTSE1 in G2/M progression after G2 checkpoint.
R-HSA-8854050. FBXL7 down-regulates AURKA during mitotic entry and in early mitosis.
R-HSA-8856825. Cargo recognition for clathrin-mediated endocytosis.
R-HSA-8856828. Clathrin-mediated endocytosis.
R-HSA-8863795. Downregulation of ERBB2 signaling.
R-HSA-8866652. Synthesis of active ubiquitin: roles of E1 and E2 enzymes.
R-HSA-901032. ER Quality Control Compartment (ERQC).
R-HSA-912631. Regulation of signaling by CBL.
R-HSA-917729. Endosomal Sorting Complex Required For Transport (ESCRT).
R-HSA-936440. Negative regulators of RIG-I/MDA5 signaling.
R-HSA-936964. Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon.
R-HSA-937039. IRAK1 recruits IKK complex.
R-HSA-937041. IKK complex recruitment mediated by RIP1.
R-HSA-937042. IRAK2 mediated activation of TAK1 complex.
R-HSA-937072. TRAF6 mediated induction of TAK1 complex.
R-HSA-975110. TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling.
R-HSA-975144. IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation.
R-HSA-975163. IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation.
R-HSA-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-HSA-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
R-HSA-977225. Amyloid fiber formation.
R-HSA-983168. Antigen processing: Ubiquitination & Proteasome degradation.
SIGNORiP62987.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-60S ribosomal protein L40
Alternative name(s):
CEP52
Ubiquitin A-52 residue ribosomal protein fusion product 1
Cleaved into the following 2 chains:
Gene namesi
Name:UBA52
Synonyms:UBCEP2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

HGNCiHGNC:12458. UBA52.

Subcellular locationi

Ubiquitin :

GO - Cellular componenti

  • cytosol Source: Reactome
  • cytosolic large ribosomal subunit Source: UniProtKB
  • endocytic vesicle membrane Source: Reactome
  • endosome membrane Source: Reactome
  • extracellular exosome Source: UniProtKB
  • extracellular space Source: UniProtKB
  • lysosomal membrane Source: UniProtKB
  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
  • plasma membrane Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi48K → R: No effect on HLTF-mediated polyubiquitination of PCNA. 1 Publication1
Mutagenesisi63K → R: Abolishes HLTF-mediated polyubiquitination of PCNA. 1 Publication1
Mutagenesisi65S → A: Prevents phosphorylation in case of mitophagy. 3 Publications1
Mutagenesisi65S → D: Phosphomimetic mutant that binds and activates PARK2. 1 Publication1

Organism-specific databases

OpenTargetsiENSG00000221983.

Polymorphism and mutation databases

BioMutaiUBA52.
DMDMi302393718.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003964331 – 76UbiquitinAdd BLAST76
ChainiPRO_000039643477 – 12860S ribosomal protein L40Add BLAST52

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Cross-linki27Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Cross-linki63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Modified residuei65Phosphoserine; by PINK14 Publications1
Cross-linki76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
Modified residuei98N6,N6,N6-trimethyllysineBy similarity1

Post-translational modificationi

Ubiquitin: Phosphorylated at Ser-65 by PINK1 during mitophagy. Phosphorylated ubiquitin specifically binds and activates parkin (PARK2), triggering mitophagy (PubMed:24660806, PubMed:24751536, PubMed:24784582, PubMed:25527291). Phosphorylation does not affect E1-mediated E2 charging of ubiquitin but affects discharging of E2 enzymes to form polyubiquitin chains. It also affects deubiquitination by deubiquitinase enzymes such as USP30 (PubMed:25527291).4 Publications

Keywords - PTMi

Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiP62987.
PaxDbiP62987.
PeptideAtlasiP62987.
PRIDEiP62987.
TopDownProteomicsiP62987.

PTM databases

iPTMnetiP62987.
PhosphoSitePlusiP62987.
SwissPalmiP62987.

Expressioni

Gene expression databases

BgeeiENSG00000221983.
CleanExiHS_UBA52.
ExpressionAtlasiP62987. baseline and differential.
GenevisibleiP62987. HS.

Organism-specific databases

HPAiHPA041344.
HPA049132.

Interactioni

Subunit structurei

Ribosomal protein L40 is part of the 60S ribosomal subunit. Interacts with UBQLN1 (via UBA domain).2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
DAZAP2Q150383EBI-357304,EBI-724310

Protein-protein interaction databases

BioGridi113159. 91 interactors.
IntActiP62987. 22 interactors.
MINTiMINT-1137632.
STRINGi9606.ENSP00000388107.

Structurei

Secondary structure

1128
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 7Combined sources6
Beta strandi8 – 10Combined sources3
Beta strandi12 – 16Combined sources5
Beta strandi19 – 21Combined sources3
Helixi23 – 34Combined sources12
Helixi38 – 40Combined sources3
Beta strandi41 – 45Combined sources5
Beta strandi47 – 49Combined sources3
Beta strandi54 – 56Combined sources3
Helixi57 – 59Combined sources3
Beta strandi66 – 71Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LJ5NMR-A1-76[»]
2MBHNMR-A1-76[»]
2MJBNMR-A1-76[»]
2MURNMR-B1-76[»]
2N3UNMR-B/C1-76[»]
2N3VNMR-B/C1-76[»]
2N3WNMR-B/C1-76[»]
2NBDNMR-A1-76[»]
2NBENMR-A1-76[»]
2RSUNMR-A1-76[»]
4HJKX-ray1.78A1-76[»]
4JIOX-ray3.60U1-76[»]
4P4HX-ray3.40S/T/U/W/X1-76[»]
4PIGX-ray1.95A/B/C/D1-76[»]
4PIHX-ray1.50A/B1-76[»]
4PIJX-ray1.50A/B1-75[»]
4RF0X-ray2.80B1-75[»]
4RF1X-ray2.15B1-75[»]
4S1ZX-ray3.03A/B/C/D/E1-76[»]
4UG0electron microscopy-Lm1-128[»]
4V6Xelectron microscopy5.00Cm77-128[»]
4XKLX-ray2.10A/C1-76[»]
5AJ0electron microscopy3.50Am1-128[»]
5HPKX-ray2.43B7-79[»]
5HPLX-ray2.31C/D1-77[»]
5HPSX-ray2.05B1-83[»]
5HPTX-ray2.84B/E/H5-78[»]
5J8PX-ray1.55A1-76[»]
B10-75[»]
5JBVX-ray2.10A1-76[»]
B10-75[»]
5JBYX-ray1.99A/C/E1-76[»]
B/D/F10-75[»]
ProteinModelPortaliP62987.
SMRiP62987.
ModBaseiSearch...
MobiDBiSearch...

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 ribosomal protein L40e family.Curated
Contains 1 ubiquitin-like domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0003. Eukaryota.
COG1552. LUCA.
COG5272. LUCA.
GeneTreeiENSGT00860000133747.
HOVERGENiHBG079132.
InParanoidiP62987.
KOiK02927.
OMAiKTKCGHT.
PhylomeDBiP62987.
TreeFamiTF352129.

Family and domain databases

InterProiIPR001975. Ribosomal_L40e.
IPR019956. Ubiquitin.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR000626. Ubiquitin_dom.
[Graphical view]
PfamiPF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM01377. Ribosomal_L40e. 1 hit.
SM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P62987-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL
60 70 80 90 100
EDGRTLSDYN IQKESTLHLV LRLRGGIIEP SLRQLAQKYN CDKMICRKCY
110 120
ARLHPRAVNC RKKKCGHTNN LRPKKKVK
Length:128
Mass (Da):14,728
Last modified:August 10, 2010 - v2
Checksum:i7BCB602ABEFAD02A
GO

Sequence cautioni

The sequence AAK31162 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56998 mRNA. Translation: CAA40313.1.
X56997 Genomic DNA. Translation: CAA40312.1.
X56999 mRNA. Translation: CAA40314.1.
AF348700 mRNA. Translation: AAK31162.1. Different initiation.
AC005253 Genomic DNA. Translation: AAC25582.1.
Y00361 mRNA. Translation: CAA68439.1.
CCDSiCCDS12382.1.
PIRiS34428. UQHUR.
RefSeqiNP_001029102.1. NM_001033930.2.
NP_001307946.1. NM_001321017.1.
NP_001307947.1. NM_001321018.1.
NP_001307948.1. NM_001321019.1.
NP_001307949.1. NM_001321020.1.
NP_003324.1. NM_003333.4.
UniGeneiHs.5308.

Genome annotation databases

EnsembliENST00000430157; ENSP00000396910; ENSG00000221983.
ENST00000442744; ENSP00000388107; ENSG00000221983.
ENST00000595158; ENSP00000471622; ENSG00000221983.
ENST00000595683; ENSP00000470419; ENSG00000221983.
ENST00000596273; ENSP00000471062; ENSG00000221983.
ENST00000596304; ENSP00000472264; ENSG00000221983.
ENST00000597451; ENSP00000473048; ENSG00000221983.
ENST00000598780; ENSP00000472545; ENSG00000221983.
ENST00000599551; ENSP00000470507; ENSG00000221983.
ENST00000599595; ENSP00000471464; ENSG00000221983.
GeneIDi7311.
KEGGihsa:7311.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56998 mRNA. Translation: CAA40313.1.
X56997 Genomic DNA. Translation: CAA40312.1.
X56999 mRNA. Translation: CAA40314.1.
AF348700 mRNA. Translation: AAK31162.1. Different initiation.
AC005253 Genomic DNA. Translation: AAC25582.1.
Y00361 mRNA. Translation: CAA68439.1.
CCDSiCCDS12382.1.
PIRiS34428. UQHUR.
RefSeqiNP_001029102.1. NM_001033930.2.
NP_001307946.1. NM_001321017.1.
NP_001307947.1. NM_001321018.1.
NP_001307948.1. NM_001321019.1.
NP_001307949.1. NM_001321020.1.
NP_003324.1. NM_003333.4.
UniGeneiHs.5308.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LJ5NMR-A1-76[»]
2MBHNMR-A1-76[»]
2MJBNMR-A1-76[»]
2MURNMR-B1-76[»]
2N3UNMR-B/C1-76[»]
2N3VNMR-B/C1-76[»]
2N3WNMR-B/C1-76[»]
2NBDNMR-A1-76[»]
2NBENMR-A1-76[»]
2RSUNMR-A1-76[»]
4HJKX-ray1.78A1-76[»]
4JIOX-ray3.60U1-76[»]
4P4HX-ray3.40S/T/U/W/X1-76[»]
4PIGX-ray1.95A/B/C/D1-76[»]
4PIHX-ray1.50A/B1-76[»]
4PIJX-ray1.50A/B1-75[»]
4RF0X-ray2.80B1-75[»]
4RF1X-ray2.15B1-75[»]
4S1ZX-ray3.03A/B/C/D/E1-76[»]
4UG0electron microscopy-Lm1-128[»]
4V6Xelectron microscopy5.00Cm77-128[»]
4XKLX-ray2.10A/C1-76[»]
5AJ0electron microscopy3.50Am1-128[»]
5HPKX-ray2.43B7-79[»]
5HPLX-ray2.31C/D1-77[»]
5HPSX-ray2.05B1-83[»]
5HPTX-ray2.84B/E/H5-78[»]
5J8PX-ray1.55A1-76[»]
B10-75[»]
5JBVX-ray2.10A1-76[»]
B10-75[»]
5JBYX-ray1.99A/C/E1-76[»]
B/D/F10-75[»]
ProteinModelPortaliP62987.
SMRiP62987.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi113159. 91 interactors.
IntActiP62987. 22 interactors.
MINTiMINT-1137632.
STRINGi9606.ENSP00000388107.

PTM databases

iPTMnetiP62987.
PhosphoSitePlusiP62987.
SwissPalmiP62987.

Polymorphism and mutation databases

BioMutaiUBA52.
DMDMi302393718.

Proteomic databases

EPDiP62987.
PaxDbiP62987.
PeptideAtlasiP62987.
PRIDEiP62987.
TopDownProteomicsiP62987.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000430157; ENSP00000396910; ENSG00000221983.
ENST00000442744; ENSP00000388107; ENSG00000221983.
ENST00000595158; ENSP00000471622; ENSG00000221983.
ENST00000595683; ENSP00000470419; ENSG00000221983.
ENST00000596273; ENSP00000471062; ENSG00000221983.
ENST00000596304; ENSP00000472264; ENSG00000221983.
ENST00000597451; ENSP00000473048; ENSG00000221983.
ENST00000598780; ENSP00000472545; ENSG00000221983.
ENST00000599551; ENSP00000470507; ENSG00000221983.
ENST00000599595; ENSP00000471464; ENSG00000221983.
GeneIDi7311.
KEGGihsa:7311.

Organism-specific databases

CTDi7311.
GeneCardsiUBA52.
HGNCiHGNC:12458. UBA52.
HPAiHPA041344.
HPA049132.
MIMi191321. gene.
neXtProtiNX_P62987.
OpenTargetsiENSG00000221983.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0003. Eukaryota.
COG1552. LUCA.
COG5272. LUCA.
GeneTreeiENSGT00860000133747.
HOVERGENiHBG079132.
InParanoidiP62987.
KOiK02927.
OMAiKTKCGHT.
PhylomeDBiP62987.
TreeFamiTF352129.

Enzyme and pathway databases

BioCyciZFISH:G66-32465-MONOMER.
ReactomeiR-HSA-110312. Translesion synthesis by REV1.
R-HSA-110314. Recognition of DNA damage by PCNA-containing replication complex.
R-HSA-110320. Translesion Synthesis by POLH.
R-HSA-1169091. Activation of NF-kappaB in B cells.
R-HSA-1169408. ISG15 antiviral mechanism.
R-HSA-1234176. Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha.
R-HSA-1236382. Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants.
R-HSA-1236974. ER-Phagosome pathway.
R-HSA-1253288. Downregulation of ERBB4 signaling.
R-HSA-1295596. Spry regulation of FGF signaling.
R-HSA-1358803. Downregulation of ERBB2:ERBB3 signaling.
R-HSA-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-HSA-156902. Peptide chain elongation.
R-HSA-162588. Budding and maturation of HIV virion.
R-HSA-168638. NOD1/2 Signaling Pathway.
R-HSA-168928. RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways.
R-HSA-174048. APC/C:Cdc20 mediated degradation of Cyclin B.
R-HSA-174084. Autodegradation of Cdh1 by Cdh1:APC/C.
R-HSA-174113. SCF-beta-TrCP mediated degradation of Emi1.
R-HSA-174154. APC/C:Cdc20 mediated degradation of Securin.
R-HSA-174178. APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1.
R-HSA-174184. Cdc20:Phospho-APC/C mediated degradation of Cyclin A.
R-HSA-174490. Membrane binding and targetting of GAG proteins.
R-HSA-175474. Assembly Of The HIV Virion.
R-HSA-179409. APC-Cdc20 mediated degradation of Nek2A.
R-HSA-1799339. SRP-dependent cotranslational protein targeting to membrane.
R-HSA-180534. Vpu mediated degradation of CD4.
R-HSA-180585. Vif-mediated degradation of APOBEC3G.
R-HSA-182971. EGFR downregulation.
R-HSA-187577. SCF(Skp2)-mediated degradation of p27/p21.
R-HSA-192823. Viral mRNA Translation.
R-HSA-195253. Degradation of beta-catenin by the destruction complex.
R-HSA-201681. TCF dependent signaling in response to WNT.
R-HSA-202424. Downstream TCR signaling.
R-HSA-205043. NRIF signals cell death from the nucleus.
R-HSA-209543. p75NTR recruits signalling complexes.
R-HSA-209560. NF-kB is activated and signals survival.
R-HSA-211733. Regulation of activated PAK-2p34 by proteasome mediated degradation.
R-HSA-2122947. NOTCH1 Intracellular Domain Regulates Transcription.
R-HSA-2122948. Activated NOTCH1 Transmits Signal to the Nucleus.
R-HSA-2173788. Downregulation of TGF-beta receptor signaling.
R-HSA-2173791. TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition).
R-HSA-2173795. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
R-HSA-2173796. SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription.
R-HSA-2408557. Selenocysteine synthesis.
R-HSA-2467813. Separation of Sister Chromatids.
R-HSA-2559580. Oxidative Stress Induced Senescence.
R-HSA-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-HSA-2559585. Oncogene Induced Senescence.
R-HSA-2565942. Regulation of PLK1 Activity at G2/M Transition.
R-HSA-2644606. Constitutive Signaling by NOTCH1 PEST Domain Mutants.
R-HSA-2672351. Stimuli-sensing channels.
R-HSA-2691232. Constitutive Signaling by NOTCH1 HD Domain Mutants.
R-HSA-2871837. FCERI mediated NF-kB activation.
R-HSA-2894862. Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants.
R-HSA-2979096. NOTCH2 Activation and Transmission of Signal to the Nucleus.
R-HSA-3134975. Regulation of innate immune responses to cytosolic DNA.
R-HSA-3322077. Glycogen synthesis.
R-HSA-349425. Autodegradation of the E3 ubiquitin ligase COP1.
R-HSA-3769402. Deactivation of the beta-catenin transactivating complex.
R-HSA-3785653. Myoclonic epilepsy of Lafora.
R-HSA-382556. ABC-family proteins mediated transport.
R-HSA-400253. Circadian Clock.
R-HSA-445989. TAK1 activates NFkB by phosphorylation and activation of IKKs complex.
R-HSA-446652. Interleukin-1 signaling.
R-HSA-450302. activated TAK1 mediates p38 MAPK activation.
R-HSA-450321. JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1.
R-HSA-450408. AUF1 (hnRNP D0) binds and destabilizes mRNA.
R-HSA-4608870. Asymmetric localization of PCP proteins.
R-HSA-4641257. Degradation of AXIN.
R-HSA-4641258. Degradation of DVL.
R-HSA-4641263. Regulation of FZD by ubiquitination.
R-HSA-5205685. Pink/Parkin Mediated Mitophagy.
R-HSA-532668. N-glycan trimming in the ER and Calnexin/Calreticulin cycle.
R-HSA-5357905. Regulation of TNFR1 signaling.
R-HSA-5357956. TNFR1-induced NFkappaB signaling pathway.
R-HSA-5358346. Hedgehog ligand biogenesis.
R-HSA-5362768. Hh mutants that don't undergo autocatalytic processing are degraded by ERAD.
R-HSA-5607761. Dectin-1 mediated noncanonical NF-kB signaling.
R-HSA-5607764. CLEC7A (Dectin-1) signaling.
R-HSA-5610780. Degradation of GLI1 by the proteasome.
R-HSA-5610783. Degradation of GLI2 by the proteasome.
R-HSA-5610785. GLI3 is processed to GLI3R by the proteasome.
R-HSA-5632684. Hedgehog 'on' state.
R-HSA-5654726. Negative regulation of FGFR1 signaling.
R-HSA-5654727. Negative regulation of FGFR2 signaling.
R-HSA-5654732. Negative regulation of FGFR3 signaling.
R-HSA-5654733. Negative regulation of FGFR4 signaling.
R-HSA-5655862. Translesion synthesis by POLK.
R-HSA-5656121. Translesion synthesis by POLI.
R-HSA-5656169. Termination of translesion DNA synthesis.
R-HSA-5658442. Regulation of RAS by GAPs.
R-HSA-5668541. TNFR2 non-canonical NF-kB pathway.
R-HSA-5675221. Negative regulation of MAPK pathway.
R-HSA-5675482. Regulation of necroptotic cell death.
R-HSA-5676590. NIK-->noncanonical NF-kB signaling.
R-HSA-5678895. Defective CFTR causes cystic fibrosis.
R-HSA-5684264. MAP3K8 (TPL2)-dependent MAPK1/3 activation.
R-HSA-5685942. HDR through Homologous Recombination (HRR).
R-HSA-5687128. MAPK6/MAPK4 signaling.
R-HSA-5689603. UCH proteinases.
R-HSA-5689877. Josephin domain DUBs.
R-HSA-5689880. Ub-specific processing proteases.
R-HSA-5689896. Ovarian tumor domain proteases.
R-HSA-5689901. Metalloprotease DUBs.
R-HSA-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-HSA-5693607. Processing of DNA double-strand break ends.
R-HSA-5696394. DNA Damage Recognition in GG-NER.
R-HSA-5696395. Formation of Incision Complex in GG-NER.
R-HSA-5696397. Gap-filling DNA repair synthesis and ligation in GG-NER.
R-HSA-5696400. Dual Incision in GG-NER.
R-HSA-6781823. Formation of TC-NER Pre-Incision Complex.
R-HSA-6781827. Transcription-Coupled Nucleotide Excision Repair (TC-NER).
R-HSA-6782135. Dual incision in TC-NER.
R-HSA-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-HSA-6783310. Fanconi Anemia Pathway.
R-HSA-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.
R-HSA-6804756. Regulation of TP53 Activity through Phosphorylation.
R-HSA-6804757. Regulation of TP53 Degradation.
R-HSA-6804760. Regulation of TP53 Activity through Methylation.
R-HSA-6807004. Negative regulation of MET activity.
R-HSA-68827. CDT1 association with the CDC6:ORC:origin complex.
R-HSA-68949. Orc1 removal from chromatin.
R-HSA-69017. CDK-mediated phosphorylation and removal of Cdc6.
R-HSA-69229. Ubiquitin-dependent degradation of Cyclin D1.
R-HSA-69231. Cyclin D associated events in G1.
R-HSA-69298. Association of licensing factors with the pre-replicative complex.
R-HSA-69481. G2/M Checkpoints.
R-HSA-69541. Stabilization of p53.
R-HSA-69601. Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
R-HSA-72689. Formation of a pool of free 40S subunits.
R-HSA-72706. GTP hydrolysis and joining of the 60S ribosomal subunit.
R-HSA-72764. Eukaryotic Translation Termination.
R-HSA-8849469. PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1.
R-HSA-8852276. The role of GTSE1 in G2/M progression after G2 checkpoint.
R-HSA-8854050. FBXL7 down-regulates AURKA during mitotic entry and in early mitosis.
R-HSA-8856825. Cargo recognition for clathrin-mediated endocytosis.
R-HSA-8856828. Clathrin-mediated endocytosis.
R-HSA-8863795. Downregulation of ERBB2 signaling.
R-HSA-8866652. Synthesis of active ubiquitin: roles of E1 and E2 enzymes.
R-HSA-901032. ER Quality Control Compartment (ERQC).
R-HSA-912631. Regulation of signaling by CBL.
R-HSA-917729. Endosomal Sorting Complex Required For Transport (ESCRT).
R-HSA-936440. Negative regulators of RIG-I/MDA5 signaling.
R-HSA-936964. Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon.
R-HSA-937039. IRAK1 recruits IKK complex.
R-HSA-937041. IKK complex recruitment mediated by RIP1.
R-HSA-937042. IRAK2 mediated activation of TAK1 complex.
R-HSA-937072. TRAF6 mediated induction of TAK1 complex.
R-HSA-975110. TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling.
R-HSA-975144. IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation.
R-HSA-975163. IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation.
R-HSA-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-HSA-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
R-HSA-977225. Amyloid fiber formation.
R-HSA-983168. Antigen processing: Ubiquitination & Proteasome degradation.
SIGNORiP62987.

Miscellaneous databases

ChiTaRSiUBA52. human.
GenomeRNAii7311.
PROiP62987.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000221983.
CleanExiHS_UBA52.
ExpressionAtlasiP62987. baseline and differential.
GenevisibleiP62987. HS.

Family and domain databases

InterProiIPR001975. Ribosomal_L40e.
IPR019956. Ubiquitin.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR000626. Ubiquitin_dom.
[Graphical view]
PfamiPF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM01377. Ribosomal_L40e. 1 hit.
SM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRL40_HUMAN
AccessioniPrimary (citable) accession number: P62987
Secondary accession number(s): P02248
, P02249, P02250, P14793, P62988, Q29120, Q6LBL4, Q6LDU5, Q8WYN8, Q91887, Q91888, Q9BWD6, Q9BX98, Q9UEF2, Q9UEG1, Q9UEK8, Q9UPK7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: August 10, 2010
Last modified: November 30, 2016
This is version 125 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Miscellaneous

Ubiquitin is encoded by 4 different genes. UBA52 and RPS27A genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively. UBB and UBC genes code for a polyubiquitin precursor with exact head to tail repeats, the number of repeats differ between species and strains.
For a better understanding, features related to ubiquitin are only indicated for the first chain.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. Ribosomal proteins
    Ribosomal proteins families and list of entries
  5. SIMILARITY comments
    Index of protein domains and families

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.