Detailed view for PF3D7_1365900

Basic information

TDR Targets ID: 2320
Plasmodium falciparum, ubiquitin-60S ribosomal protein L40
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 10.5461 | Length (AA): 128 | MW (Da): 14617 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG2

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF00240   Ubiquitin family
PF01020   Ribosomal L40e family

Gene Ontology

Mouse over links to read term descriptions.
GO:0031386   protein tag  
GO:0005840   ribosome  
GO:0005622   intracellular  
GO:0005515   protein binding  
GO:0003735   structural constituent of ribosome  
GO:0006511   ubiquitin-dependent protein catabolic process  
GO:0006412   translation  

Metabolic Pathways

Ribosome (KEGG)

Structural information

Modbase 3D models:

There are 6 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
1 71 1sif (A) 1 71 89.00 0 1 1.74 -2.35
1 89 1wia (A) 163 249 26.00 0 1 1.02 -0.42
1 76 2jvc (A) 6 81 82.00 0 1 1.62795 -1.22
1 90 2k25 (A) 9 98 82.00 0.0000022 1 1.58753 -0.03
39 76 1wx8 (A) 55 92 45.00 0.48 0.92 0.829075 0.02
79 126 2ayj (A) 5 49 49.00 0.0073 0.84 0.8262 0.55

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, merozoite, sporozoite, early ring, early schizont, early trophozoite, late ring, late schizont, late trophozoite, Oocyst, Ring, Sporozoite, Female Gametocyte, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Show/Hide expression data references
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.

Orthologs

Ortholog group members (OG5_128257)

Species Accession Gene Product
Arabidopsis thaliana AT2G36170   60S ribosomal protein L40-1
Arabidopsis thaliana AT3G52590   ubiquitin extension protein 1
Babesia bovis BBOV_IV003190   ubiquitin / ribosomal protein CEP52
Brugia malayi Bm1_54210   ubiquitin-like protein
Caenorhabditis elegans CELE_ZK1010.1   Protein UBQ-2
Cryptosporidium hominis Chro.70260   ubiquitin / ribosomal protein CEP52
Cryptosporidium parvum cgd7_2280   60S ribosomal protein L40
Dictyostelium discoideum DDB_G0280755   ubiquitin/ribosomal protein L40 fusion protein
Drosophila melanogaster Dmel_CG2960   Ribosomal protein L40
Echinococcus granulosus EgrG_000887700   ribosomal protein L40
Echinococcus multilocularis EmuJ_000887700   ribosomal protein L40
Homo sapiens ENSG00000221983   ubiquitin A-52 residue ribosomal protein fusion product 1
Leishmania braziliensis LbrM.31.2130   ubiquitin-fusion protein
Leishmania braziliensis LbrM.31.2290   ubiquitin-fusion protein
Leishmania braziliensis LbrM.31.2110   ubiquitin-fusion protein
Leishmania infantum LinJ.31.1930   ubiquitin-fusion protein
Leishmania infantum LinJ.31.2070   ubiquitin-fusion protein
Leishmania major LmjF.31.1900   ubiquitin-fusion protein
Leishmania major LmjF.31.2030   ubiquitin-fusion protein
Loa Loa (eye worm) LOAG_05875   ubiquitin/ribosomal fusion protein
Mus musculus 216818   predicted gene 4802
Mus musculus ENSMUSG00000090137   ubiquitin A-52 residue ribosomal protein fusion product 1
Neospora caninum NCLIV_042000   ubiquitin / ribosomal protein CEP52 fusion protein, putative
Oryza sativa 4332169   Os03g0234200
Oryza sativa 4332312   Os03g0259500
Onchocerca volvulus OVOC8926  
Plasmodium berghei PBANKA_1141700   ubiquitin-60S ribosomal protein L40, putative
Plasmodium falciparum PF3D7_1365900   ubiquitin-60S ribosomal protein L40
Plasmodium knowlesi PKNH_1105400   ubiquitin-60S ribosomal protein L40, putative
Plasmodium vivax PVX_115255   ubiquitin-60S ribosomal protein L40, putative
Saccharomyces cerevisiae YIL148W   ubiquitin-ribosomal 60S subunit protein L40A fusion protein
Saccharomyces cerevisiae YKR094C   ubiquitin-ribosomal 60S subunit protein L40B fusion protein
Schistosoma japonicum Sjp_0200460   ko:K02927 large subunit ribosomal protein L40e, putative
Schistosoma mansoni Smp_089430   ubiquitin (ribosomal protein L40)
Toxoplasma gondii TGME49_289750   ribosomal-ubiquitin protein RPL40
Theileria parva TP01_1070   ubiquitin/ribosomal fusion protein, putative
Trichomonas vaginalis TVAG_110140   ubiquitin, putative
Trichomonas vaginalis TVAG_331660   ubiquitin, putative
Trichomonas vaginalis TVAG_184140   ubiquitin, putative
Trichomonas vaginalis TVAG_141620   ubiquitin, putative
Trichomonas vaginalis TVAG_457430   ubiquitin 1, putative
Trichomonas vaginalis TVAG_184180   ubiquitin 1, putative
Trichomonas vaginalis TVAG_019240   ubiquitin, putative
Trichomonas vaginalis TVAG_174190   ubiquitin, putative

Essentiality

PF3D7_1365900 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_ZK1010.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_ZK1010.1 Caenorhabditis elegans larval arrest wormbase
CELE_ZK1010.1 Caenorhabditis elegans sterile wormbase
TGME49_289750 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier PF3D7_1365900 (Plasmodium falciparum), ubiquitin-60S ribosomal protein L40
Title for this comment
Comment