Detailed view for PF3D7_0507100

Basic information

TDR Targets ID: 4102
Plasmodium falciparum, 60S ribosomal protein L4
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 11.1958 | Length (AA): 411 | MW (Da): 46211 | Paralog Number: 0

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

Druggability Group : DG1

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

PF00573   Ribosomal protein L4/L1 family
PF14374   60S ribosomal protein L4 C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005622   intracellular  
GO:0015934   large ribosomal subunit  
GO:0005840   ribosome  
GO:0003735   structural constituent of ribosome  
GO:0003723   RNA binding  
GO:0006412   translation  

Metabolic Pathways

Ribosome (KEGG)

Structural information

Modbase 3D models:

There are 4 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
8 260 1vq8 (C) 3 243 39.00 0 1 1.05 0.05
7 263 1vq8 (C) 2 246 37.00 0 1 1.0499 -0.01
266 398 4uos (A) 7 132 31.00 0.036 0.72 0.528601 -0.19
345 410 4tql (A) 91 157 24.00 0.064 0 0.495184 -1.11

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:

PDB tag
  • 3J79:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5UMD:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

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, Female Gametocyte, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Sporozoite. Zanghi G
Show/Hide expression data references
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.

Orthologs

Ortholog group members (OG5_127050)

Species Accession Gene Product
Arabidopsis thaliana AT3G09630   60S ribosomal protein L4-1
Arabidopsis thaliana AT5G02870   60S ribosomal protein L4-2
Babesia bovis BBOV_II006110   ribosomal protein RPL4A
Brugia malayi Bm1_14285   60S ribosomal protein L4
Candida albicans CaO19.7217   likely cytosolic ribosomal protein similar to S. cerevisiae RPL4A (YBR031W) and RPL4B (YDR012W) large subunit protein L4
Caenorhabditis elegans CELE_B0041.4   Protein RPL-4
Cryptosporidium hominis Chro.60371   60S ribosomal protein-like
Cryptosporidium hominis Chro.60369   hypothetical protein
Cryptosporidium parvum cgd6_3190   60S ribosomal protein-like, putative
Dictyostelium discoideum DDB_G0277803   60S ribosomal protein L4
Drosophila melanogaster Dmel_CG5502   Ribosomal protein L4
Echinococcus granulosus EgrG_000860300   ribosomal protein l4
Entamoeba histolytica EHI_064710   60S ribosomal protein L4, putative
Entamoeba histolytica EHI_194270   60S ribosomal protein L4, putative
Entamoeba histolytica EHI_035440   60S ribosomal protein L4, putative
Entamoeba histolytica EHI_000510   60S ribosomal protein L4, putative
Echinococcus multilocularis EmuJ_000860300   ribosomal protein l4
Giardia lamblia GL50803_17547   Ribosomal protein L4
Homo sapiens 6124   ribosomal protein L4
Leishmania braziliensis LbrM.29.1180   ribosomal protein L1a, putative
Leishmania braziliensis LbrM.29.1150   ribosomal protein L1a, putative
Leishmania donovani LdBPK_291160.1   ribosomal protein L1a, putative
Leishmania infantum LinJ.29.1170   ribosomal protein L1a, putative
Leishmania infantum LinJ.29.1160   ribosomal protein L1a, putative
Leishmania infantum LinJ.29.1180   ribosomal protein L1a, putative
Leishmania major LmjF.29.1070   ribosomal protein L1a, putative
Leishmania major LmjF.29.1080   ribosomal protein L1a, putative
Leishmania major LmjF.29.1090   ribosomal protein L1a, putative
Leishmania mexicana LmxM.08_29.1090   ribosomal protein L1a, putative
Leishmania mexicana LmxM.08_29.1070   ribosomal protein L1a, putative
Loa Loa (eye worm) LOAG_00227   60S ribosomal protein L4
Mus musculus ENSMUSG00000032399   ribosomal protein L4
Neospora caninum NCLIV_053580   50S ribosomal protein L4P, related
Oryza sativa 9272589   Os03g0796501
Oryza sativa 4342563   Os07g0180900
Plasmodium berghei PBANKA_1106700   60S ribosomal protein L4, putative
Plasmodium falciparum PF3D7_0507100   60S ribosomal protein L4
Plasmodium knowlesi PKNH_1026500   60S ribosomal protein L4, putative
Plasmodium vivax PVX_097915   60S ribosomal protein L4, putative
Plasmodium yoelii PY06225   ribosomal protein L4/L1 family, putative
Saccharomyces cerevisiae YDR012W   ribosomal 60S subunit protein L4B
Saccharomyces cerevisiae YBR031W   ribosomal 60S subunit protein L4A
Schistosoma japonicum Sjp_0062490   ko:K02930 large subunit ribosomal protein L4e, putative
Schistosoma mansoni Smp_153790   60S ribosomal protein L4
Schmidtea mediterranea mk4.000687.05   Putative 60s ribosomal protein L4
Schmidtea mediterranea mk4.000363.05   Putative 60s ribosomal protein L4
Trypanosoma brucei gambiense Tbg972.3.5660   60S ribosomal protein L4
Trypanosoma brucei gambiense Tbg972.3.5650   60S ribosomal protein L4
Trypanosoma brucei Tb927.3.5050   60S ribosomal protein L4
Trypanosoma cruzi TcCLB.509995.10   60S ribosomal protein L4, putative
Trypanosoma cruzi TcCLB.504121.30   60S ribosomal protein L4, putative
Toxoplasma gondii TGME49_309120   ribosomal protein RPL4
Theileria parva TP02_0568   60S ribosomal protein L4/L1, putative
Trichomonas vaginalis TVAG_164550   60S ribosomal protein L4, putative
Trichomonas vaginalis TVAG_128790   60S ribosomal protein L4, putative
Trichomonas vaginalis TVAG_476810   60S ribosomal protein L4, putative
Trichomonas vaginalis TVAG_189110   60S ribosomal protein L4, putative

Essentiality

PF3D7_0507100 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.3.5050 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.3.5050 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.3.5050 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.3.5050 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_B0041.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_B0041.4 Caenorhabditis elegans sterile wormbase
TGME49_309120 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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.
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170

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.

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Gene identifier PF3D7_0507100 (Plasmodium falciparum), 60S ribosomal protein L4
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