9V1K | pdb_00009v1k

Cryo- EM structure of small subunit (head) of 75S ribosome with P- tRNA from Entamoeba histolytica


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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Literature

Cryo-EM structure of ribosome from pathogenic protozoa Entamoeba histolytica reveals unique features of its architecture.

Sharma, S.Mishra, S.Gourinath, S.Kaushal, P.S.

(2025) Nat Commun 16: 7758-7758

  • DOI: https://doi.org/10.1038/s41467-025-62767-x
  • Primary Citation of Related Structures:  
    9V1I, 9V1J, 9V1K, 9V1L, 9V21, 9V24, 9V25, 9V26, 9V27, 9V28, 9V29

  • PubMed Abstract: 

    Entamoeba histolytica, an anaerobic protozoan parasite, is the causative agent of amoebiasis, bloody diarrhea, and liver abscesses in humans. Amoebiasis is more predominant in tropical areas with poor sanitation conditions, and it remains the fourth leading cause of death due to a protozoan infection. E. histolytica life cycle spans between an infective 'cyst stage' and an active disease-causing 'trophozoite stage'. We have isolated ribosomes from the trophozoite stage of E. histolytica. Here, we report single particle cryo-EM structures of the 53S ribosome large subunit (LSU), and 75S associated ribosomes, with P-tRNA, A/P and P/E tRNAs, and with paromomycin antibiotic, at 2.8 Å to 3.4 Å resolution. The E. histolytica possesses a reduced ribosome with a conserved core, and the periphery evolved with species-specific unique features. The most notable features are the presence of the rRNA triple helix near the peptide exit tunnel, the expansion segment H88ES102 near the exit site on LSU, and unique insertions in r-proteins. Furthermore, the 75S ribosome paromomycin complex structure provides the atomic details of its interactions. These structures provide insights into the evolutionary adaptation of the E. histolytica translational machinery and may be explored further for amoebicidal therapeutic intervention.


  • Organizational Affiliation
    • Structural Biology & Translation Regulation laboratory, UNESCO-DBT Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana (Delhi-NCR), India.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25A [auth sA]137Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4M9F4 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28, putativeB [auth sD]69Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4LZQ8 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S29, putativeC [auth sE]56Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4LW10 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta 2-like 1, putativeD [auth sG]321Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4LTS8 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3F [auth sd]244Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4LT02 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7G [auth sg]206Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for O15587 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10, putativeH [auth sl]127Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4LVC0 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15, putativeI [auth sq]144Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4M7H3 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16, putativeJ [auth ss]158Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4M2R7 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17, putativeK [auth st]117Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4M0Z2 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13L [auth su]155Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for P48151 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19M [auth sv]155Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for O15631 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20, putativeN [auth sw]118Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4M5V7 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 5
MoleculeChains LengthOrganismImage
17S rRNAE [auth sa]1,947Entamoeba histolytica HM-1:IMSS
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.4
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/PR45101/DRUG/134/121/2022

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release