Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0007699
UniProt IDP62987
Primary gene name(s)UBA52
Synonym gene name(s)UBCEP2
Protein nameUbiquitin-60S ribosomal protein L40
Protein functionUbiquitin: 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.; FUNCTION: 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.
Subcellular locationUbiquitin: Cytoplasm {ECO:0000250}. Nucleus {ECO:0000250}.;
SUBCELLULAR LOCATION: 60S ribosomal protein L40: Cytoplasm {ECO:0000250}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P62987
Gene Ontology
(Biological Process)
Complete annatation
activation of MAPK activity [GO:0000187];
anaphase-promoting complex-dependent catabolic process [GO:0031145];
cellular protein metabolic process [GO:0044267];
cellular protein modification process [GO:0006464];
DNA damage response, detection of DNA damage [GO:0042769];
DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest [GO:0006977];
endosomal transport [GO:0016197];
ERBB2 signaling pathway [GO:0038128];
error-free translesion synthesis [GO:0070987];
error-prone translesion synthesis [GO:0042276];
Fc-epsilon receptor signaling pathway [GO:0038095];
fibroblast growth factor receptor signaling pathway [GO:0008543];
G2/M transition of mitotic cell cycle [GO:0000086];
global genome nucleotide-excision repair [GO:0070911];
glycogen biosynthetic process [GO:0005978];
I-kappaB kinase/NF-kappaB signaling [GO:0007249];
innate immune response [GO:0045087];
interstrand cross-link repair [GO:0036297];
intracellular transport of virus [GO:0075733];
ion transmembrane transport [GO:0034220];
JNK cascade [GO:0007254];
macroautophagy [GO:0016236];
MAPK cascade [GO:0000165];
MyD88-dependent toll-like receptor signaling pathway [GO:0002755];
MyD88-independent toll-like receptor signaling pathway [GO:0002756];
negative regulation of apoptotic process [GO:0043066];
negative regulation of canonical Wnt signaling pathway [GO:0090090];
negative regulation of epidermal growth factor receptor signaling pathway [GO:0042059];
negative regulation of transcription from RNA polymerase II promoter [GO:0000122];
negative regulation of transforming growth factor beta receptor signaling pathway [GO:0030512];
negative regulation of type I interferon production [GO:0032480];
negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle [GO:0051436];
NIK/NF-kappaB signaling [GO:0038061];
Notch signaling pathway [GO:0007219];
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay [GO:0000184];
nucleotide-binding oligomerization domain containing signaling pathway [GO:0070423];
nucleotide-excision repair, DNA damage recognition [GO:0000715];
nucleotide-excision repair, DNA duplex unwinding [GO:0000717];
nucleotide-excision repair, DNA gap filling [GO:0006297];
nucleotide-excision repair, DNA incision [GO:0033683];
nucleotide-excision repair, DNA incision, 5'-to lesion [GO:0006296];
nucleotide-excision repair, preincision complex assembly [GO:0006294];
positive regulation of apoptotic process [GO:0043065];
positive regulation of canonical Wnt signaling pathway [GO:0090263];
positive regulation of epidermal growth factor receptor signaling pathway [GO:0045742];
positive regulation of I-kappaB kinase/NF-kappaB signaling [GO:0043123];
positive regulation of NF-kappaB transcription factor activity [GO:0051092];
positive regulation of transcription from RNA polymerase II promoter [GO:0045944];
positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition [GO:0051437];
proteasome-mediated ubiquitin-dependent protein catabolic process [GO:0043161];
protein polyubiquitination [GO:0000209];
protein ubiquitination involved in ubiquitin-dependent protein catabolic process [GO:0042787];
regulation of mRNA stability [GO:0043488];
regulation of necrotic cell death [GO:0010939];
regulation of signal transduction by p53 class mediator [GO:1901796];
regulation of transcription from RNA polymerase II promoter in response to hypoxia [GO:0061418];
regulation of tumor necrosis factor-mediated signaling pathway [GO:0010803];
regulation of type I interferon production [GO:0032479];
rRNA processing [GO:0006364];
SRP-dependent cotranslational protein targeting to membrane [GO:0006614];
stimulatory C-type lectin receptor signaling pathway [GO:0002223];
stress-activated MAPK cascade [GO:0051403];
T cell receptor signaling pathway [GO:0050852];
transcription-coupled nucleotide-excision repair [GO:0006283];
transforming growth factor beta receptor signaling pathway [GO:0007179];
translation [GO:0006412];
translational initiation [GO:0006413];
translesion synthesis [GO:0019985];
TRIF-dependent toll-like receptor signaling pathway [GO:0035666];
tumor necrosis factor-mediated signaling pathway [GO:0033209];
viral life cycle [GO:0019058];
viral transcription [GO:0019083];
virion assembly [GO:0019068];
Wnt signaling pathway [GO:0016055];
Wnt signaling pathway, planar cell polarity pathway [GO:0060071]
Gene Ontology
(Molecular Function)
Complete annatation
structural constituent of ribosome [GO:0003735]
Gene Ontology
(Cellular Component)
Complete annatation
cytosol [GO:0005829];
cytosolic large ribosomal subunit [GO:0022625];
endocytic vesicle membrane [GO:0030666];
endosome membrane [GO:0010008];
extracellular exosome [GO:0070062];
extracellular space [GO:0005615];
lysosomal membrane [GO:0005765];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
plasma membrane [GO:0005886];
ribosome [GO:0005840]
Protein-protein interaction113159
Phylogenetic treeP62987
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
Brass et al., Science, 2008
Smith et al., J. Immunol, 2010
gene status
Lu et al., J. Virol., 2011
      Folds changes 8h: unknown; Folds changes 16h: unknown; Tested: unknown;
Schoggins JW and Rice CM, Curr. Opin. Virol., 2011
      Targeted viruses: unknown
      Viral life cycle: unknown
      Mechanism related to antiviral activity: unknown
Anti-viral restriction factor Liu et al., Retrovirology, 2011
      unknown (Triplicates)

Gene Expression Profile       top

            Up-regulated;            Down-regulated

For brief introduction to each study, please go to the help page.

Gene expression during HIV latency

(1). Mohammadi et al., PLoS Pathog., 2014

Differentially expressed transcripts (Pairwise) during latency and subsequent viral reactivation using several agents - Primary CD4+ T-cell based model

DMSO: Dimethyl suloxyde (negative control) - 0.0033% final
SAHA: Vorinostat (Histone deacetylase inhibitor) - 0.5 μM
CD3: TCR Stimulation by IL-2+ antiCD3/anti-CD28 antibodies
IL7: Interleukin-7 based stimulation
DISU: Disulfiram (alcohol dehydrogenase inhibitor) - 0.5 μM
AZA: 5-azacytidine (AZA; DNA methylation inhibitor) - 1 μM
Experimental Condition Log2 Fold Change P value Adjusted P value
AZA vs. CD3-0.1563456577822410.6323748318037630.731758423412385
AZA vs. DISU0.07521746674725630.765532311439480.976021571236163
AZA vs. IL7-0.1251231630670880.5134952840536870.999311006273513
AZA vs. SAHA-0.06435717767282090.7912915031019640.945044626544454
DISU vs. CD30.218313949400450.5464461632087680.665895672126837
DISU vs. IL7-0.2099020931992990.4035699156691390.764731878124468
DISU vs. SAHA-0.1369566771073810.6375407871179830.887363982513402
DMSO vs. AZA0.1197693147474450.4723433029805811
DMSO vs. CD30.2612174368334820.4135084626993630.52765585215703
DMSO vs. DISU0.04171207329941680.8638555370800790.984706040690414
DMSO vs. IL7-0.2372636859443830.1852881825832910.698245959661933
DMSO vs. SAHA-0.1887272786250130.4220824546930280.761273895964411
HIV vs. Mock in Activation-0.1853915878755870.7663407185820740.999983755607037
HIV vs. Mock in Latency-0.2279206886565420.1654150745400820.999834320637052
IL7 vs. CD30.03768021519132290.9064952014580710.940695502346128
SAHA vs. CD30.06883405053451810.845254921058590.890519551199171
SAHA vs. IL70.05859678294529640.8092801981561040.917500730069578
(2). Iglesias-Ussel et al., J. Virol., 2013

Up and Downregulated transcripts during Latency (Latently infected CD4+ T cells vs Uninfected)- Primary CD4+Tcell based model
Log2 Fold Change P Value
unknown unknown

Gene expression during HIV infection and replication

(1). Imbeault et al., PloS Pathog., 2012

Transcriptomic profiling of HIV-1 infected CD4+ T cells - Primary CD4+ T cells
Experiment type Log2 Fold Change P Value Adjusted P Value
Infected vs. Mock unknown unknown unknown
Infected vs. Bystander unknown unknown unknown
(2). Lefebvre et al., J. Virol., 2011

Transcriptome analysis of T-cell line (Sup T1)
Log2 Fold Change unknown
(3). Li et al., J. Immunol., 2013

Lymphatic tissue
Acute Fold Change Acute P Value Asymt Fold Change Asypt P Value AIDS Fold Change AIDS P Value
unknown unknown unknown unknown unknown unknown
(4). Chang et al., MBio., 2011

Transcriptome analysis of T-cell line (Sup T1)

Derived from Sherrill-Mix et al., BMC Retrovirol., 2015 cross validation
Up-regulated (True) unknown
(5). Sherrill-Mix et al., BMC Retrovirol., 2015

Deep RNA-seq analysis of primary human T cell infected with low passage HIV isolate HIV89.6 - Primary CD4+ T cell based
Test Status Log2 Fold Change P Value
OK -0.386846 0.00221059
(6). Rotger et al., PLoS Pathog., 2010

Genome-wide mRNA expression of CD4+ T cells from HIV-infected patient
(Genes differentially expressed (at adjusted p<0.01) according to the empirical Bayes approach)
Log2 Fold Change P Value
unknown unknown

Proteomic/Transcriptomics studies indicating differentially expressed genes mediated by HIV

(1). Greenwood et al., Elife, 2016

Activated (CD3/CD28) Primary human CD4+ T cells infected with pNL4-3-dE-EGFP. The table shows the complete (unfiltered) TMT (tandem mass tag)-based proteomic time course dataset
6 h 24 h 48 h 72 h RTi
1.012 0.93 0.866 0.808 0.908
(2). Navare et al., Virology, 2012

SUP-T1 cell line
FC-4hpi P-value FC-8hpi P-value FC-20hpi P-value Category
unknown unknown unknown unknown unknown unknown unknown
(3). Hyrcza et al., J. Virolo., 2007

Primary human CD4+ and CD8+ T Cells
Affymetrix Prob ID Fold Change In CD8? Category
unknown unknown unknown unknown

Protein Overview       top

Drug-protein Interaction       (annotations from DrugBank)      top

not found

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
2LJ5 NMR - A=1-76.
2MBH NMR - A=1-76.
2MJB NMR - A=1-76.
2MUR NMR - B=1-76.
2N3U NMR - B/C=1-76.
2N3V NMR - B/C=1-76.
2N3W NMR - B/C=1-76.
2NBD NMR - A=1-76.
2NBE NMR - A=1-76.
2RSU NMR - A=1-76.
4HJK X-ray 1.7Å A=1-76.
4JIO X-ray 3.6Å U=1-76.
4P4H X-ray 3.4Å S/T/U/W/X=1-76.
4PIG X-ray 1.9Å A/B/C/D=1-76.
4PIH X-ray 1.5Å A/B=1-76.
4PIJ X-ray 1.5Å A/B=1-75.
4RF0 X-ray 2.8Å B=1-75.
4RF1 X-ray 2.1Å B=1-75.
4S1Z X-ray 3.0Å A/B/C/D/E=1-76.
4UG0 EM - Lm=1-128.
4V6X EM 5.0Å Cm=77-128.
4XKL X-ray 2.1Å A/C=1-76.
5AJ0 EM 3.5Å Am=1-128.
5HPK X-ray 2.4Å B=7-79.
5HPL X-ray 2.3Å C/D=1-77.
5HPS X-ray 2.0Å B=1-83.
5HPT X-ray 2.8Å B/E/H=5-78.
5J8P X-ray 1.5Å A=1-76# B=10-75.
5JBV X-ray 2.1Å A=1-76# B=10-75.
5JBY X-ray 1.9Å A/C/E=1-76# B/D/F=10-75.

HIV-1 Interaction       (annotations from NCBI HIV-1 Interaction Database)      top

HIV Partner Interaction Type PubMed
Pr55(Gag) incorporates 25631074
Vpr upregulates 23874603

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03010 Ribosome - Homo sapiens (human)