Detailed view for PF3D7_1013100

Basic information

TDR Targets ID: 1204
Plasmodium falciparum, U3 small nucleolar RNA-associated protein 13, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 6.449 | Length (AA): 1220 | MW (Da): 144605 | 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

PF00400   WD domain, G-beta repeat
PF08625   Utp13 specific WD40 associated domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0032040   small subunit processome  
GO:0005515   protein binding  
GO:0006364   rRNA processing  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 11 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
67 1064 3bta (A) 196 1276 19.00 0.000013 1 0.77 1.2
589 887 1got (B) 68 340 15.00 0 1 0.37 -0.51
398 887 2ymu (A) 7 495 18.00 0 1 0.432239 1.09
727 808 3ow8 (A) 185 267 32.00 0.0041 0.63 0.509913 -0.85
731 804 3jro (A) 8 86 46.00 0.046 0.98 0.568356 -0.25
731 804 4l9o (A) 2019 2097 43.00 0.07 0.98 0.564356 -0.51
364 888 2ymu (A) 33 577 18.00 0 1 0.483975 0.78
728 809 3ow8 (A) 185 267 32.00 0.0041 0.63 0.510558 -0.85
732 805 3jro (A) 8 86 46.00 0.047 0.98 0.569006 -0.25
732 805 4l9o (A) 2019 2097 43.00 0.07 0.98 0.565006 -0.51
1035 1210 4u5a (C) 49 239 18.00 0.63 0.18 0.195144 -0.01

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 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, gametocyte, merozoite, sporozoite, early ring, early trophozoite, late ring, Ring, Sporozoite, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 48 hs, late trophozoite, Oocyst. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 40 hs, Male Gametocyte. Otto TD 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.
  • 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.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB

Orthologs

Ortholog group members (OG5_128119)

Species Accession Gene Product
Arabidopsis thaliana AT5G16750   WD-40 repeat protein TOZ
Babesia bovis BBOV_II006870   WD domain, G-beta repeat containing protein
Brugia malayi Bm1_43000   MGC69179 protein
Candida albicans CaO19.4268   similar to S. cerevisiae YLR222C
Candida albicans CaO19.11744   similar to S. cerevisiae YLR222C
Caenorhabditis elegans CELE_Y53C12B.1   Protein Y53C12B.1
Cryptosporidium hominis Chro.40108   similar to WD40-repeat protein
Cryptosporidium hominis Chro.40109   similar to transducin beta-like 3; WD-repeat protein SAZD
Cryptosporidium parvum cgd4_900   WD repeat containing protein
Dictyostelium discoideum DDB_G0276283   U3 small nucleolar ribonucleoprotein
Drosophila melanogaster Dmel_CG1671   CG1671 gene product from transcript CG1671-RA
Echinococcus granulosus EgrG_001180500   transducin beta protein 3
Entamoeba histolytica EHI_140750   WD domain containing protein
Echinococcus multilocularis EmuJ_001180500   transducin beta protein 3
Giardia lamblia GL50803_15487   WD-40 repeat protein
Homo sapiens ENSG00000183751   transducin (beta)-like 3
Leishmania braziliensis LbrM.25.0380   hypothetical protein, conserved
Leishmania donovani LdBPK_250440.1   WD domain, G-beta repeat/Utp13 specific WD40 associated domain containing protein, putative
Leishmania infantum LinJ.25.0440   hypothetical protein, conserved
Leishmania major LmjF.25.0430   hypothetical protein, conserved
Leishmania mexicana LmxM.25.0430   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_05625   hypothetical protein
Mus musculus 213773   transducin (beta)-like 3
Oryza sativa 4336833   Os04g0592700
Onchocerca volvulus OVOC9954  
Plasmodium berghei PBANKA_1211500   U3 small nucleolar RNA-associated protein 13, putative
Plasmodium falciparum PF3D7_1013100   U3 small nucleolar RNA-associated protein 13, putative
Plasmodium knowlesi PKNH_0812900   U3 small nucleolar RNA-associated protein 13, putative
Plasmodium vivax PVX_094875   hypothetical protein, conserved
Plasmodium yoelii PY01359   hypothetical protein
Saccharomyces cerevisiae YLR222C   Utp13p
Schistosoma japonicum Sjp_0046360   U3 small nucleolar RNA-associated protein 13, putative
Schistosoma mansoni Smp_050470   hypothetical protein
Schmidtea mediterranea mk4.031167.01  
Schmidtea mediterranea mk4.013254.00  
Trypanosoma brucei gambiense Tbg972.11.370   hypothetical protein, conserved,predicted WD40 repeat protein
Trypanosoma brucei Tb927.11.460   predicted WD40 repeat protein
Trypanosoma brucei Tb11.v5.0726   WD domain, G-beta repeat/Utp13 specific WD40 associated domain containing protein, putative
Trypanosoma congolense TcIL3000.11.400   predicted WD40 repeat protein
Trypanosoma cruzi TcCLB.507093.170   hypothetical protein, conserved
Theileria parva TP02_0662   hypothetical protein
Trichomonas vaginalis TVAG_288620   WD-repeat protein, putative

Essentiality

PF3D7_1013100 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.03.0680 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.03.0680 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.03.0680 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.03.0680 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_Y53C12B.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_Y53C12B.1 Caenorhabditis elegans slow growth wormbase
YLR222C Saccharomyces cerevisiae inviable yeastgenome
Show/Hide essentiality data references
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.

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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User comments

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Gene identifier PF3D7_1013100 (Plasmodium falciparum), U3 small nucleolar RNA-associated protein 13, putative
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