Detailed view for PF3D7_1104200

Basic information

TDR Targets ID: 1532
Plasmodium falciparum, chromatin remodeling protein
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 6.5033 | Length (AA): 1426 | MW (Da): 167441 | 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

PF00176   SNF2 family N-terminal domain
PF00271   Helicase conserved C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0016589   NURF complex  
GO:0006355   regulation of transcription, DNA-dependent  
GO:0016585   chromatin remodeling complex  
GO:0016887   ATPase activity  
GO:0008094   DNA-dependent ATPase activity  
GO:0008026   ATP-dependent helicase activity  
GO:0005524   ATP binding  
GO:0004386   helicase activity  
GO:0003677   DNA binding  
GO:0003676   nucleic acid binding  
GO:0006338   chromatin remodeling  
GO:0043044   ATP-dependent chromatin remodeling  

Metabolic Pathways

Purine metabolism (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
262 880 1z3i (X) 94 735 26.00 0 1 0.45 -0.78
616 779 1t5i (A) 263 428 19.00 0.00000076 0.96 0.48 -1.45
1 233 3na7 (A) 5 226 10.00 0.18 0.01 0.293094 -1.01
3 169 2ap3 (A) 16 194 13.00 0.3 0 0.283811 -1.09
135 781 3mwy (W) 183 866 35.00 0.0000000063 1 0.809317 0.24
308 826 3mwy (W) 362 899 47.00 0 1 0.837755 -0.09
855 1390 4un4 (B) 468 1059 15.00 0.64 0.71 0.302477 1.44
1121 1302 4uos (A) 1 186 19.00 0.0092 0.39 0.42223 -1.36
1177 1281 2nog (A) 794 896 23.00 0.39 0.51 0.361333 -0.59
1194 1364 2y9y (A) 870 1009 29.00 0.037 0.48 0.115716 0.87
1206 1426 4tql (A) 9 236 14.00 0.000074 0.02 0.257679 -0.13
13 200 3na7 (A) 10 193 14.00 0.19 0 0.33883 -1.18
135 849 3mwy (W) 183 922 35.00 0.000000019 1 0.820554 0.37
168 249 3ult (A) 13 99 30.00 0.32 0.03 0.507844 -2.12
312 778 1z63 (A) 434 883 35.00 0 1 0.738019 -0.45
1132 1295 4uos (A) 2 180 20.00 0.025 0.78 0.373888 -1.15
1193 1414 4tql (A) 9 238 19.00 0.00066 0.79 0.392589 -0.52
1193 1363 2y9y (A) 870 1009 29.00 0.037 0.48 0.1163 0.87

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, merozoite, sporozoite, early ring, late ring, Oocyst, Ring, Sporozoite. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 48 hs, early schizont, early trophozoite, late schizont. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 40 hs, late trophozoite, Female Gametocyte. Otto TD PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Male Gametocyte. Lasonder E
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_127117)

Species Accession Gene Product
Arabidopsis thaliana AT5G18620   chromatin remodeling factor17
Arabidopsis thaliana AT3G06400   chromatin-remodeling protein 11
Babesia bovis BBOV_IV008380   SNF2 helicase, putative
Brugia malayi Bm1_02485   Potential global transcription activator SNF2L, putative
Candida albicans CaO19.7401   ATPase
Candida albicans CaO19.4437   chromosome structure
Candida albicans CaO19.11916   chromosome structure
Caenorhabditis elegans CELE_F37A4.8   Protein ISW-1
Cryptosporidium hominis Chro.60441   hypothetical protein
Cryptosporidium hominis Chro.80323   chromatin remodelling complex protein SNF2L
Cryptosporidium parvum cgd8_2770   SNF2L ortholog with a SWI/SNF2 like ATpase and a Myb domain
Cryptosporidium parvum cgd6_3860   SNF2 helicase, putative
Dictyostelium discoideum DDB_G0292948   ATP-dependent chromatin-remodelling factor
Drosophila melanogaster Dmel_CG8625   Imitation SWI
Echinococcus granulosus EgrG_001187700   SWI:SNF matrix associated
Entamoeba histolytica EHI_044890   helicase, putative
Echinococcus multilocularis EmuJ_001187700   SWI:SNF matrix associated
Giardia lamblia GL50803_8228   DNA-dependent ATPase, putative
Homo sapiens ENSG00000153147   SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5
Homo sapiens ENSG00000102038   SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1
Leishmania braziliensis LbrM.33.1970   transcription activator,DNA-dependent ATPase, putative
Leishmania donovani LdBPK_331800.1   chromatin-remodeling complex atpase chain iswi
Leishmania infantum LinJ.33.1800   transcription activator,DNA-dependent ATPase, putative
Leishmania major LmjF.33.1700   transcription activator,DNA-dependent ATPase, putative
Leishmania mexicana LmxM.32.1700   transcription activator,DNA-dependent ATPase, putative
Loa Loa (eye worm) LOAG_06686   transcription activator
Mus musculus ENSMUSG00000031099   SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1
Mus musculus 93762   SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5
Neospora caninum NCLIV_004490   hypothetical protein
Neospora caninum NCLIV_033850   hypothetical protein
Oryza sativa 4325731   Os01g0367900
Oryza sativa 4337825   Os05g0150300
Plasmodium berghei PBANKA_0942700   chromatin remodeling protein, putative
Plasmodium falciparum PF3D7_1104200   chromatin remodeling protein
Plasmodium knowlesi PKNH_0901800   chromatin remodeling protein, putative
Plasmodium vivax PVX_090890   helicase, putative
Plasmodium yoelii PY02376   SNF2 family N-terminal domain, putative
Saccharomyces cerevisiae YBR245C   chromatin-remodeling ATPase ISW1
Saccharomyces cerevisiae YOR304W   Isw2p
Schistosoma japonicum Sjp_0053770   ko:K01529 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 [EC:3.6.1.-], putati
Schistosoma mansoni Smp_008830   helicase
Schmidtea mediterranea mk4.001620.04   Chromatin-remodeling complex ATPase chain isw-1
Schmidtea mediterranea mk4.000783.09   Chromatin-remodeling complex ATPase chain isw-1
Schmidtea mediterranea mk4.000775.16  
Schmidtea mediterranea mk4.003083.00  
Trypanosoma brucei gambiense Tbg.972.2.360   transcription activator, putative
Trypanosoma brucei Tb927.2.1810   chromatin-remodeling complex atpase chain iswi
Trypanosoma congolense TcIL3000_2_50   chromatin-remodeling complex atpase chain iswi
Trypanosoma cruzi TcCLB.509213.170   chromatin-remodeling complex atpase chain iswi
Trypanosoma cruzi TcCLB.507265.15   ISWI complex protein
Toxoplasma gondii TGME49_273870   SWI2/SNF2 ISWI-like (AT hook)
Toxoplasma gondii TGME49_321440   SWI2/SNF2 ISWI-like SANT
Theileria parva TP01_0936   DNA-dependent ATPase, putative

Essentiality

PF3D7_1104200 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.2.1810 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.2.1810 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.2.1810 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.2.1810 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F37A4.8 Caenorhabditis elegans embryonic lethal wormbase
CELE_F37A4.8 Caenorhabditis elegans larval arrest wormbase
CELE_F37A4.8 Caenorhabditis elegans larval lethal wormbase
CELE_F37A4.8 Caenorhabditis elegans slow growth wormbase
CELE_F37A4.8 Caenorhabditis elegans sterile wormbase
PBANKA_0942700 Plasmodium berghei Essential plasmo
TGME49_321440 Toxoplasma gondii Probably essential sidik
TGME49_273870 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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

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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Gene identifier PF3D7_1104200 (Plasmodium falciparum), chromatin remodeling protein
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