Detailed view for PF3D7_0218500

Basic information

TDR Targets ID: 3447
Plasmodium falciparum, small nuclear ribonucleoprotein Sm D2, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 10.3401 | Length (AA): 101 | MW (Da): 11714 | 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

PF01423   LSM domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0030532   small nuclear ribonucleoprotein complex  
GO:0005681   spliceosome  
GO:0008380   RNA splicing  

Metabolic Pathways

Spliceosome (KEGG)

Structural information

Modbase 3D models:

There are 4 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
11 99 1th7 (A) 3 78 32.00 0 1 1.15 -0.3
17 100 1b34 (B) 27 113 72.00 0 1 1.5 -0.92
1 101 4pjo (D) 11 114 60.00 0 1 1.6786 -0.58
2 99 3pgw (Y) 8 112 66.00 0 1 1.6142 0.37

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

Orthologs

Ortholog group members (OG5_127733)

Species Accession Gene Product
Arabidopsis thaliana AT3G62840   small nuclear ribonucleoprotein D2
Arabidopsis thaliana AT2G47640   small nuclear ribonucleoprotein D2
Babesia bovis BBOV_I004230   small nuclear ribonucleoprotein, putative
Brugia malayi Bm1_52920   Chain B, Crystal Structure Of The D1d2 Sub-Complex From The Human Snrnp Core Domain.
Caenorhabditis elegans CELE_C52E4.3   Protein SNR-4
Cryptosporidium hominis Chro.40363   small nuclear ribonucleoprotein
Cryptosporidium parvum cgd4_3190   small nuclear ribonucleoprotein
Dictyostelium discoideum DDB_G0285395   LSM domain-containing protein
Drosophila melanogaster Dmel_CG1249   Small ribonucleoprotein particle protein SmD2
Echinococcus granulosus EgrG_000458700   small nuclear ribonucleoprotein Sm
Entamoeba histolytica EHI_108640   LSM domain containing protein
Echinococcus multilocularis EmuJ_000458700   small nuclear ribonucleoprotein Sm
Giardia lamblia GL50803_32297   Small nuclear ribonucleoprotein Sm D2, putative
Homo sapiens ENSG00000125743   small nuclear ribonucleoprotein D2 polypeptide 16.5kDa
Leishmania braziliensis LbrM.33.3460   small nuclear ribonucleoprotein SmD2
Leishmania donovani LdBPK_333340.1   small nuclear ribonucleoprotein SmD2
Leishmania infantum LinJ.33.3340   small nuclear ribonucleoprotein SmD2
Leishmania major LmjF.33.3190   small nuclear ribonucleoprotein SmD2
Leishmania mexicana LmxM.32.3190   small nuclear ribonucleoprotein SmD2
Loa Loa (eye worm) LOAG_06277   small Nuclear Ribonucleoprotein family member
Mus musculus 107686   small nuclear ribonucleoprotein D2
Neospora caninum NCLIV_035950   hypothetical protein
Oryza sativa 4338385   Os05g0314100
Plasmodium berghei PBANKA_0315200   small nuclear ribonucleoprotein Sm D2, putative
Plasmodium falciparum PF3D7_0218500   small nuclear ribonucleoprotein Sm D2, putative
Plasmodium knowlesi PKNH_0402400   small nuclear ribonucleoprotein Sm D2, putative
Plasmodium vivax PVX_002615   small nuclear ribonucleoprotein Sm D2, putative
Plasmodium yoelii PY01248   small nuclear ribonucleoprotein.
Saccharomyces cerevisiae YLR275W   Smd2p
Schistosoma japonicum Sjp_0055670   Probable small nuclear ribonucleoprotein Sm D2, putative
Schistosoma mansoni Smp_075560   small nuclear ribonucleoprotein Sm D2
Schmidtea mediterranea mk4.003577.06   Probable small nuclear ribonucleoprotein Sm D2
Schmidtea mediterranea mk4.004232.01   Probable small nuclear ribonucleoprotein Sm D2
Trypanosoma brucei gambiense Tbg.972.2.4110   small nuclear ribonucleoprotein SmD2
Trypanosoma brucei Tb927.2.5850   small nuclear ribonucleoprotein SmD2
Trypanosoma congolense TcIL3000_2_1520   small nuclear ribonucleoprotein SmD2, putative
Trypanosoma cruzi TcCLB.511189.80   small nuclear ribonucleoprotein SmD2, putative
Trypanosoma cruzi TcCLB.508667.49   small nuclear ribonucleoprotein SmD2, putative
Toxoplasma gondii TGME49_270830   small nuclear ribonucleoprotein
Theileria parva TP02_0729   small nuclear ribonucleoprotein D2, putative
Trichomonas vaginalis TVAG_472580   small nuclear ribonucleoprotein sm D2, putative

Essentiality

PF3D7_0218500 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.2.5850 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.2.5850 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.2.5850 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.2.5850 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C52E4.3 Caenorhabditis elegans embryonic arrest wormbase
CELE_C52E4.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_C52E4.3 Caenorhabditis elegans larval arrest wormbase
CELE_C52E4.3 Caenorhabditis elegans slow growth wormbase
CELE_C52E4.3 Caenorhabditis elegans sterile wormbase
YLR275W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0315200 Plasmodium berghei Dispensable plasmo
TGME49_270830 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • 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.
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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_0218500 (Plasmodium falciparum), small nuclear ribonucleoprotein Sm D2, putative
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