Detailed view for PF3D7_0627300

Basic information

TDR Targets ID: 4622
Plasmodium falciparum, E3 ubiquitin-protein ligase RNF5, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 4.6104 | Length (AA): 449 | MW (Da): 52812 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 1

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

PF13920   Zinc finger, C3HC4 type (RING finger)

Gene Ontology

Mouse over links to read term descriptions.
GO:0008270   zinc ion binding  
GO:0005515   protein binding  

Structural information

Modbase 3D models:

There are 14 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
279 363 2ckl (A) 8 92 19.00 0 0.78 0.38 -0.49
290 331 1chc () 8 50 40.00 0.000015 1 0.58 -0.26
4 115 2oto (A) 69 184 6.00 0.22 0 0.249443 -0.18
8 133 4r61 (A) 10 149 9.00 0.13 0 0.444624 -1.22
261 369 4ayc (B) 374 483 17.00 0.022 0.25 0.545062 -1.4
263 332 3zni (A) 345 416 26.00 0.52 1 0.506202 -0.33
287 328 1rmd (A) 23 65 40.00 0.066 0.99 0.534141 0.28
289 338 4tkp (B) 14 70 43.00 0.95 0.71 0.353659 0.36
10 129 2oto (A) 65 184 12.00 0.21 0 0.349156 0
12 171 4u5a (C) 48 238 21.00 0.0058 0.01 0.549242 -0.83
259 367 4ayc (A) 374 483 21.00 0.0099 0.26 0.567148 -1.2
285 326 1rmd (A) 23 65 40.00 0.065 0.99 0.53466 0.28
287 336 4tkp (B) 14 70 43.00 0.51 0.71 0.354157 0.36
288 336 2ecw (A) 22 76 35.00 0.11 1 0.46432 -0.35

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, Oocyst, Ring, Sporozoite, Male Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Female Gametocyte. Lasonder E
Show/Hide expression data references
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • 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_128528)

Species Accession Gene Product
Arabidopsis thaliana AT2G23780   RING/U-box superfamily protein
Arabidopsis thaliana AT2G42030   putative zinc ion binding protein
Arabidopsis thaliana AT2G44410   RING/U-box domain-containing protein
Arabidopsis thaliana AT1G19310   RING/U-box superfamily protein
Babesia bovis BBOV_III009770   hypothetical protein
Brugia malayi Bm1_56615   Hypothetical RING finger protein C16C10.7 in chromosome III
Caenorhabditis elegans CELE_C16C10.7   Protein RNF-5
Cryptosporidium parvum cgd2_1820   hypothetical protein
Dictyostelium discoideum DDB_G0285333   hypothetical protein
Drosophila melanogaster Dmel_CG32581   CG32581 gene product from transcript CG32581-RB
Drosophila melanogaster Dmel_CG8974   CG8974 gene product from transcript CG8974-RD
Echinococcus granulosus EgrG_001014900   RING finger protein 185
Entamoeba histolytica EHI_038330   zinc finger domain containing protein
Echinococcus multilocularis EmuJ_001014900   RING finger protein 185
Homo sapiens ENSG00000138942   ring finger protein 185
Homo sapiens ENSG00000204308   ring finger protein 5, E3 ubiquitin protein ligase
Loa Loa (eye worm) LOAG_06910   hypothetical protein
Mus musculus ENSMUSG00000020448   ring finger protein 185
Mus musculus ENSMUSG00000015478   ring finger protein 5
Neospora caninum NCLIV_020050   Zinc finger (C3HC4 RING finger) protein, related
Oryza sativa 4325492   Os01g0766200
Oryza sativa 4344731   Os08g0162400
Oryza sativa 4333714   Os03g0678400
Oryza sativa 4352888   Os12g0636000
Plasmodium berghei PBANKA_1126000   E3 ubiquitin-protein ligase RNF5, putative
Plasmodium falciparum PF3D7_0627300   E3 ubiquitin-protein ligase RNF5, putative
Plasmodium knowlesi PKNH_1122500   E3 ubiquitin-protein ligase RNF5, putative
Plasmodium vivax PVX_114470   E3 ubiquitin-protein ligase RNF5, putative
Plasmodium yoelii PY04641   similar to CG8974 gene product-related
Schistosoma japonicum Sjp_0305250   ko:K10666 E3 ubiquitin-protein ligase RNF5, putative
Schistosoma mansoni Smp_026260   rnf5
Schmidtea mediterranea mk4.009801.00   Putative rnf5
Schmidtea mediterranea mk4.005312.01  
Trypanosoma brucei gambiense Tbg972.10.7780   hypothetical protein, conserved
Trypanosoma brucei Tb927.10.6380   ring finger containing protein
Toxoplasma gondii TGME49_205600   zinc finger, C3HC4 type (RING finger) domain-containing protein
Theileria parva TP04_0895   hypothetical protein
Trichomonas vaginalis TVAG_482150   conserved hypothetical protein

Essentiality

PF3D7_0627300 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.6380 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.6380 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.6380 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.6380 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
TGME49_205600 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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_0627300 (Plasmodium falciparum), E3 ubiquitin-protein ligase RNF5, putative
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