Detailed view for PF3D7_1108600

Basic information

TDR Targets ID: 1575
Plasmodium falciparum, endoplasmic reticulum-resident calcium binding protein
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 4.2514 | Length (AA): 343 | MW (Da): 39374 | Paralog Number: 0

Signal peptide: Y | 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

PF13202   EF hand
PF13499   EF-hand domain pair

Gene Ontology

Mouse over links to read term descriptions.
GO:0005783   endoplasmic reticulum  
GO:0005509   calcium ion binding  
GO:0006886   intracellular protein transport  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 7 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
41 202 2aao (A) 6 160 22.00 0 1 0.67 0.09
131 203 1n0y (B) 76 147 25.00 0.00000011 0.93 0.65 -1.2
34 199 4ik8 (A) 281 445 29.00 0.0000011 1 0.720165 0.26
135 197 4cpv (A) 38 102 35.00 0.16 1 0.698873 -1.03
144 202 1xo5 (A) 112 178 39.00 0.092 1 0.735212 -1.41
144 197 1tiz (A) 7 59 42.00 0.22 0.37 0.452634 0.14
28 235 2be4 (A) 23 262 31.00 0.0023 1 0.687314 0.71

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, early schizont, Oocyst, Ring, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile sporozoite, early ring, early trophozoite, late ring, late schizont, late trophozoite, Male Gametocyte. PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Sporozoite. Zanghi G
Show/Hide expression data references
  • 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.
  • 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_129808)

Species Accession Gene Product
Arabidopsis thaliana AT5G08580   EF-hand, calcium binding motif-containing protein
Arabidopsis thaliana AT4G27790   Calcium-binding EF hand family protein
Babesia bovis BBOV_III007520   membrane-associated calcum-binding protein, putative
Brugia malayi Bm1_55540   EF hand family protein
Caenorhabditis elegans CELE_M03F4.7   Protein CALU-1, isoform B
Cryptosporidium hominis Chro.20427   membrane-associated calcum-binding protein
Cryptosporidium parvum cgd2_3990   protein with signal peptide, ER retention motif and 4x EF hands
Drosophila melanogaster Dmel_CG9148   supercoiling factor
Echinococcus granulosus EgrG_000245300   calumenin
Echinococcus multilocularis EmuJ_000245300   calumenin
Homo sapiens 813   calumenin
Loa Loa (eye worm) LOAG_05293   EF hand family protein
Mus musculus ENSMUSG00000029767   calumenin
Neospora caninum NCLIV_030420   Rcn2-prov protein, related
Oryza sativa 4337432   Os04g0681500
Plasmodium berghei PBANKA_0938400   endoplasmic reticulum-resident calcium binding protein, putative
Plasmodium falciparum PF3D7_1108600   endoplasmic reticulum-resident calcium binding protein
Plasmodium knowlesi PKNH_0906200   endoplasmic reticulum-resident calcium binding protein, putative
Plasmodium vivax PVX_091105   endoplasmic reticulum-resident calcium binding protein, putative
Plasmodium yoelii PY05050   membrane-associated calcum-binding protein
Schistosoma japonicum Sjp_0032650   IPR002048,Calcium-binding EF-hand,domain-containing
Schistosoma japonicum Sjp_0025210   Calumenin precursor, putative
Schistosoma japonicum Sjp_0072720   Reticulocalbin-1 precursor, putative
Schistosoma mansoni Smp_103740.2   calmodulin related calcium binding protein
Schistosoma mansoni Smp_103740.1   calmodulin related calcium binding protein
Schistosoma mansoni Smp_005230.1   reticulocalbin
Schistosoma mansoni Smp_005230.3   reticulocalbin
Schistosoma mansoni Smp_005230.2   reticulocalbin
Schmidtea mediterranea mk4.016806.00   Reticulocalbin-2
Schmidtea mediterranea mk4.005455.00   Calumenin-like protein
Schmidtea mediterranea mk4.001404.06  
Schmidtea mediterranea mk4.002060.02   Calumenin-like protein
Schmidtea mediterranea mk4.001100.05  
Schmidtea mediterranea mk4.003282.02  
Schmidtea mediterranea mk4.001284.04  
Toxoplasma gondii TGME49_229480   calcium binding protein precursor, putative
Theileria parva TP04_0681   membrane-associated calcium-binding protein, putative

Essentiality

PF3D7_1108600 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_M03F4.7 Caenorhabditis elegans larval arrest wormbase
CELE_M03F4.7 Caenorhabditis elegans larval lethal wormbase
TGME49_229480 Toxoplasma gondii Probably non-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
  • 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.
  • 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
  • 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.
  • 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

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): 0.1

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
Species Target Length Identity Alignment span Linked Drugs Reference
Bos taurus Calmodulin 149 aa 28.0% 132 aa Compounds References
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.

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Gene identifier PF3D7_1108600 (Plasmodium falciparum), endoplasmic reticulum-resident calcium binding protein
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