Detailed view for PF3D7_0409600

Basic information

TDR Targets ID: 3874
Plasmodium falciparum, replication protein A1, large subunit
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.0167 | Length (AA): 1145 | MW (Da): 134202 | Paralog Number: 0

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

Druggability Group : DG3

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

PF01336   OB-fold nucleic acid binding domain
PF08646   Replication factor-A C terminal domain
PF16900   Replication protein A OB domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005662   DNA replication factor A complex  
GO:0003676   nucleic acid binding  
GO:0006261   DNA-dependent DNA replication  
GO:0006260   DNA replication  

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
682 924 1jmc (A) 183 420 34.00 0 1 0.56 -0.33
683 792 1ynx (A) 184 294 37.00 0 1 0.59 -0.39
940 1133 1l1o (C) 440 611 24.00 0 1 0.27 0.22
511 629 4o0a (A) 0 120 8.00 0.51 0 0.20273 -0.97
683 792 1ynx (A) 184 294 37.00 0.000000000017 0.98 0.57887 -0.26
684 924 1jmc (A) 185 420 35.00 0.0000000011 1 0.61728 -0.05
684 1134 4gnx (C) 183 621 26.00 0 1 0.589686 0.86
686 1126 4gnx (C) 185 620 30.00 0 1 0.615953 0.78
940 1134 1l1o (C) 440 612 24.00 0 1 0.192806 0.77
510 628 4o0a (A) 0 120 8.00 0.71 0 0.202921 -0.95
679 792 1ynx (A) 181 294 34.00 0.002 0.99 0.53455 -0.22
683 1133 4gnx (C) 183 621 27.00 0 1 0.603131 0.85
684 923 1jmc (A) 186 420 35.00 0.00000000005 1 0.60669 0.07
939 1133 1l1o (C) 440 612 24.00 0 1 0.201955 0.68

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, Sporozoite. PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, early schizont, late trophozoite, Oocyst. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 8 hs, gametocyte, early trophozoite, late schizont, Female Gametocyte, Male Gametocyte. Otto TD PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Ring. Zanghi G
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.
  • 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.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

Orthologs

Ortholog group members (OG5_127539)

Species Accession Gene Product
Arabidopsis thaliana AT5G45400   replication protein RPA70C
Arabidopsis thaliana AT2G06510   replication factor A 1A
Arabidopsis thaliana AT5G61000   replication protein A 70 kDa DNA-binding subunit D
Arabidopsis thaliana AT5G08020   RPA70-kDa subunit B
Arabidopsis thaliana AT4G19130   Replication factor-A protein 1-related
Babesia bovis BBOV_III010480   replication factor-a protein 1 (rpa1) family protein
Brugia malayi Bm1_18390   replication factor A 73 kDa subunit
Candida albicans CaO19.2093   similar to single-stranded DNA binding protein involved in DNA-damage repair
Candida albicans CaO19.9640   similar to single-stranded DNA binding protein involved in DNA-damage repair
Caenorhabditis elegans CELE_F18A1.5   Protein RPA-1
Cryptosporidium hominis Chro.70509   replication protein A 70kDa
Cryptosporidium parvum cgd7_4620   Rf-A (OB fold protein)
Dictyostelium discoideum DDB_G0289513   OB fold-containing protein, nucleic acid binding
Drosophila melanogaster Dmel_CG9633   Replication Protein A 70
Echinococcus granulosus EgrG_000714700   replication protein A 70 kDa DNA binding
Entamoeba histolytica EHI_062980   replication factor A protein 1, putative
Echinococcus multilocularis EmuJ_000714700   replication protein A 70 kDa DNA binding
Homo sapiens ENSG00000132383   replication protein A1, 70kDa
Leishmania braziliensis LbrM.28.1990   replication factor A, 51kDa subunit, putative
Leishmania donovani LdBPK_281940.1   Replication factor A protein 1
Leishmania infantum LinJ.28.1940   replication factor A, 51kDa subunit, putative
Leishmania major LmjF.28.1820   replication factor A, 51kDa subunit, putative
Leishmania mexicana LmxM.28.1820   replication factor A, 51kDa subunit, putative
Loa Loa (eye worm) LOAG_09949   replication factor A 73 kDa subunit
Mus musculus ENSMUSG00000000751   replication protein A1
Neospora caninum NCLIV_050400   hypothetical protein
Oryza sativa 4330902   Os02g0776800
Oryza sativa 4332052   Os03g0214100
Oryza sativa 4337594   Os05g0111000
Onchocerca volvulus OVOC9194   Putative replication factor A 73 kDa subunit
Plasmodium berghei PBANKA_1007200   replication protein A1, large subunit, putative
Plasmodium falciparum PF3D7_0409600   replication protein A1, large subunit
Plasmodium knowlesi PKNH_0307700   replication protein A1, large subunit, putative
Plasmodium vivax PVX_000765   replication protein A1, large subunit, putative
Plasmodium yoelii PY04090   putative replication A protein
Saccharomyces cerevisiae YAR007C   Rfa1p
Schistosoma japonicum Sjp_0015650   ko:K07466 replication factor A1, putative
Schistosoma mansoni Smp_121800   replication factor A 1 rfa1
Schmidtea mediterranea mk4.003115.03  
Schmidtea mediterranea mk4.003115.02  
Schmidtea mediterranea mk4.003630.01  
Trypanosoma brucei gambiense Tbg972.11.10200   replication factor A, 51kDa subunit, putative
Trypanosoma brucei Tb927.11.9130   Replication factor A protein 1
Trypanosoma congolense TcIL3000.11.9490   Replication factor A protein 1
Trypanosoma cruzi TcCLB.510901.60   Replication factor A protein 1
Toxoplasma gondii TGME49_236080   replication factor-a protein 1 (rpa1) subfamily protein
Theileria parva TP02_0095   replication factor A protein, putative
Trichomonas vaginalis TVAG_060460   replication factor A 1, rfa1, putative
Trichomonas vaginalis TVAG_226230   replication factor A 1, rfa1, putative
Trichomonas vaginalis TVAG_294830   replication factor A 1, rfa1, putative
Trichomonas vaginalis TVAG_433860   replication factor A 1, rfa1, putative

Essentiality

PF3D7_0409600 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.0870 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.01.0870 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.0870 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb11.01.0870 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F18A1.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_F18A1.5 Caenorhabditis elegans sterile wormbase
YAR007C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1007200 Plasmodium berghei Slow plasmo
TGME49_236080 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • 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
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • 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.
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource

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
Species Known druggable target Linked compounds Reference
Homo sapiens replication protein A1, 70kDa Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0092 0.3901 0.5
0.0187 0.418 1
0.0148 0.3476 0.5
0.0151 0.3901 0.5
0.0364 0.4659 1
0.0058 0.3476 0.5
0.0399 0.4182 0.5
0.0137 0.3901 0.5
0.005 0.3476 0.5
0.0066 0.3901 0.5
0.043 0.2563 1
0.0431 0.4678 1
0.0024 0.277 0.5
0.0084 0.4182 1
0.047 0.2769 1
0.0326 0.3476 1
0.0422 0.4736 1
0.0423 0.4678 1
0.0086 0.3046 1
0.0405 0.4734 1
0.0059 0.4181 1
0.0326 0.3476 1
0.0199 0.4234 0.5
0.048 0.4596 1
0.0091 0.3901 0.5
0.0182 0.4234 0.5
0.0433 0.4678 1
0.0165 0.4234 0.5
0.0165 0.4085 0.5
0.0423 0.4732 1
0.0502 0.437 0.5
0.0182 0.4234 0.5
0.0094 0.3901 0.5

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_0409600 (Plasmodium falciparum), replication protein A1, large subunit
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