9V1J | pdb_00009v1j

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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 S26A [auth sB]144Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4M7G9 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS27B [auth sC]84Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for P38654 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2F [auth sb]254Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4M5A0 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5G [auth sc]255Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4M7U0 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1H [auth se]256Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4M609 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, putativeI [auth sf]326Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4LYF4 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6J [auth sh]266Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4LXN2 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7K [auth si]201Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4M9F9 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8L [auth sj]237Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4M8Y8 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4M [auth sk]185Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for O15612 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11, putativeN [auth sm]156Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4M979 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13, putativeO [auth so]151Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for A0A175JJM9 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S14, putativeP [auth sp]146Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for B1N2I3 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15a, putativeQ [auth sr]130Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21R [auth sx]86Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4LWW3 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23, putativeS [auth sy]141Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4M5B7 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24, putativeT [auth sz]140Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4M549 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 3
MoleculeChains LengthOrganismImage
P-tRNAC [auth sH]76Entamoeba histolytica HM-1:IMSS
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Entity ID: 4
MoleculeChains LengthOrganismImage
mRNAD [auth sK]6Entamoeba histolytica HM-1:IMSS
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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: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.4
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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