Detailed view for PF3D7_1235300

Basic information

TDR Targets ID: 5394
Plasmodium falciparum, CCR4-NOT transcription complex subunit 4, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.818 | Length (AA): 1662 | MW (Da): 194674 | 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

PF14570   RING/Ubox like zinc-binding domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0008270   zinc ion binding  
GO:0005515   protein binding  
GO:0003676   nucleic acid binding  
GO:0000166   nucleotide binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 18 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
113 189 1e4u (A) 2 78 43.00 0 1 0.49 0.75
334 423 1p27 (B) 66 148 24.00 0.000000025 0.91 0.47 -1.76
334 431 2cpi (A) 102 198 51.00 0.00000000095 1 0.73 -0.98
341 441 1p1t (A) 16 109 16.00 0.00000000018 0.8 0.34 -1.21
123 186 1e4u (A) 12 75 52.00 0.000000076 1 0.613408 0.29
125 172 5aie (A) 33 82 63.00 0.00000011 1 0.740781 -0.38
192 295 3ult (A) 12 113 28.00 0.043 0.03 0.489475 -1.7
334 430 2cpi (A) 102 197 51.00 0 1 0.651263 -0.09
742 884 2ap3 (A) 43 194 27.00 0.19 0.08 0.488941 -2.31
1139 1353 4uos (A) 1 180 34.00 0.26 0.7 0.335262 -0.42
1259 1487 4tql (A) 9 235 16.00 0.0069 0.01 0.300886 -0.46
1466 1653 2ap3 (A) 9 196 18.00 0.52 0.12 0.279217 -0.78
123 188 1e4u (A) 12 77 50.00 0.000052 1 0.5466 0.59
192 292 3ult (A) 12 113 29.00 0.11 0.02 0.461712 -1.75
331 427 2cpi (A) 102 197 51.00 0 1 0.651288 -0.09
720 886 2ap3 (A) 22 194 24.00 0.16 0.07 0.461712 -2
1141 1355 4uos (A) 1 180 34.00 0.27 0.7 0.335803 -0.42
1395 1584 4uos (A) 1 183 15.00 0.0092 0.03 0.254652 -0.84

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 sporozoite, Oocyst, Ring, Sporozoite, Female Gametocyte, Male Gametocyte. PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, merozoite, early ring, early trophozoite, late ring. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, gametocyte, late schizont, late trophozoite. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile early schizont. PlasmoDB
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.
  • 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_127674)

Species Accession Gene Product
Arabidopsis thaliana AT3G45630   RNA binding (RRM/RBD/RNP motifs) family protein
Arabidopsis thaliana AT2G28540   RNA recognition motif-containing protein
Arabidopsis thaliana AT5G60170   RNA binding (RRM/RBD/RNP motifs) family protein
Babesia bovis BBOV_IV004110   conserved hypothetical protein
Brugia malayi Bm1_39595   Not-like
Candida albicans CaO19.2379   potential RRM domain protein similar to MOT2 (YER068W) component of the cytoplasmic mRNA deadenylase and CCR4-NOT transcription
Candida albicans CaO19.9915   potential RRM domain protein similar to MOT2 (YER068W) component of the cytoplasmic mRNA deadenylase and CCR4-NOT transcription
Caenorhabditis elegans CELE_C49H3.5   Protein NTL-4, isoform B
Cryptosporidium hominis Chro.70553   protein potential transcriptional repressor Not4hp
Cryptosporidium parvum cgd7_4960   Not4hp/Mot2p, RING finger+RRM domains
Dictyostelium discoideum DDB_G0275005   RING zinc finger-containing protein
Drosophila melanogaster Dmel_CG31716   Cnot 4 homologue
Echinococcus granulosus EgrG_001028400   CCR4 NOT transcription complex subunit 4
Entamoeba histolytica EHI_080710   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_001028400   CCR4 NOT transcription complex subunit 4
Giardia lamblia GL50803_8427   Transcriptional repressor NOT4Hp, putative
Homo sapiens ENSG00000080802   CCR4-NOT transcription complex, subunit 4
Loa Loa (eye worm) LOAG_11511   CCR4-NOT transcription complex component
Loa Loa (eye worm) LOAG_14798   hypothetical protein
Mus musculus ENSMUSG00000038784   CCR4-NOT transcription complex, subunit 4
Neospora caninum NCLIV_016050   hypothetical protein
Oryza sativa 4351244   Os12g0102400
Oryza sativa 4349535   Os11g0102800
Plasmodium berghei PBANKA_1449900   CCR4-NOT transcription complex subunit 4, putative
Plasmodium falciparum PF3D7_1235300   CCR4-NOT transcription complex subunit 4, putative
Plasmodium knowlesi PKNH_1455000   CCR4-NOT transcription complex subunit 4, putative
Plasmodium vivax PVX_100715   hypothetical protein, conserved
Plasmodium yoelii PY00512   putative protein potential transcriptional repressor Not4hp
Saccharomyces cerevisiae YER068W   CCR4-NOT core ubiquitin-protein ligase subunit MOT2
Schistosoma japonicum Sjp_0037100   ko:K10643 CCR4-NOT transcription complex, subunit 4, putative
Schmidtea mediterranea mk4.000299.11  
Toxoplasma gondii TGME49_328300   hypothetical protein
Toxoplasma gondii TGME49_239410   hypothetical protein
Theileria parva TP01_0345   hypothetical protein
Trichomonas vaginalis TVAG_450320   conserved hypothetical protein
Trichomonas vaginalis TVAG_415730   conserved hypothetical protein
Trichomonas vaginalis TVAG_407280   conserved hypothetical protein

Essentiality

PF3D7_1235300 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_C49H3.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_C49H3.5 Caenorhabditis elegans slow growth wormbase
TGME49_239410 Toxoplasma gondii Probably essential sidik
TGME49_328300 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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.

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

Druggability index (range: 0 to 1): 0.5

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

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Gene identifier PF3D7_1235300 (Plasmodium falciparum), CCR4-NOT transcription complex subunit 4, putative
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