Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0002536
UniProt IDP40429
Primary gene name(s)RPL13A
Synonym gene name(s)unknown
Protein name60S ribosomal protein L13a
Protein functionAssociated with ribosomes but is not required for canonical ribosome function and has extra-ribosomal functions. Component of the GAIT, gamma interferon-activated inhibitor of translation complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma activation and subsequent phosphorylation dissociates from the ribosome and assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs, such as ceruplasmin and suppresses their translation. In the GAIT complex interacts with m7G cap-bound eIF4G at or near the eIF3-binding site and blocks the recruitment of the 43S ribosomal complex. Involved in methylation of rRNA. {ECO:0000269|PubMed:14567916, ECO:0000269|PubMed:17218275, ECO:0000269|PubMed:17921318, ECO:0000269|PubMed:23071094}.
Subcellular locationCytoplasm {ECO:0000305|PubMed:14567916}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P40429
Gene Ontology
(Biological Process)
Complete annatation
cellular response to interferon-gamma [GO:0071346];
negative regulation of formation of translation preinitiation complex [GO:1901194];
negative regulation of translation [GO:0017148];
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay [GO:0000184];
rRNA processing [GO:0006364];
SRP-dependent cotranslational protein targeting to membrane [GO:0006614];
translation [GO:0006412];
translational initiation [GO:0006413];
viral transcription [GO:0019083]
Gene Ontology
(Molecular Function)
Complete annatation
mRNA binding [GO:0003729];
poly(A RNA binding [GO:0044822];
structural constituent of ribosome [GO:0003735]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
cytosol [GO:0005829];
cytosolic large ribosomal subunit [GO:0022625];
focal adhesion [GO:0005925];
GAIT complex [GO:0097452];
intracellular ribonucleoprotein complex [GO:0030529];
large ribosomal subunit [GO:0015934];
membrane [GO:0016020];
nucleolus [GO:0005730];
nucleus [GO:0005634]
Protein-protein interaction117068
Phylogenetic treeP40429
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. CD3-0.4888391032884920.1360098730353820.224724929444121
AZA vs. DISU-0.08649643476597950.7315623458734580.974560663114398
AZA vs. IL7-0.1890416064979460.32348866137040.999311006273513
AZA vs. SAHA0.04693462962774480.8469017833205220.963550011990275
DISU vs. CD30.3898320004194730.2823902314501460.412196218541638
DISU vs. IL7-0.1116345319156350.656801736118290.901841266512228
DISU vs. SAHA0.1347871430661650.6428194507496830.889862399398225
DMSO vs. AZA-0.0396496055776880.8117747010199261
DMSO vs. CD30.4341671998967710.1747520749891570.268609326569906
DMSO vs. DISU0.04386597094870780.8568641214479710.983807945138555
DMSO vs. IL7-0.1416120634127860.4288248862011240.857268009114859
DMSO vs. SAHA0.08082058589035860.7308365333724990.921387247641323
HIV vs. Mock in Activation-0.1390600140711380.8236313650089010.999983755607037
HIV vs. Mock in Latency-0.2250910010511230.1702104096490550.999834320637052
IL7 vs. CD30.3078086700918770.3373152669097590.475395462342797
SAHA vs. CD30.5110068206013940.1485743964390320.2392878224149
SAHA vs. IL70.2324494518997660.3385288243489910.588556934305105
(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) FALSE
(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 -0.834876 0.000305467
(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
0.99 0.957 0.866 0.838 0.871
(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

Drugbank ID Drug Name Drug Status Pharmacological Action Drug Action
DB07374 Anisomycin experimental unknown unknown
DB02494 Alpha-Hydroxy-Beta-Phenyl-Propionic Acid experimental unknown unknown
DB08437 Puromycin experimental unknown unknown

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
4UG0 EM - LO=1-203.
4V6X EM 5.0Å CO=1-203.
5AJ0 EM 3.5Å AO=1-203.

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

not found

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

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