9V21 | pdb_00009v21

Cryo- EM structure of 75S ribosome with P- tRNA from Entamoeba histolytica


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2D [auth lD]246Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Find proteins for O15574 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3, putativeE [auth lE]402Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4F [auth lF]431Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Find proteins for B1N384 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5, putativeG [auth lG]286Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6H [auth lH]203Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Find proteins for O15595 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7, putativeI [auth lI]230Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aJ [auth lJ]286Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9, putativeK [auth lK]197Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10, putativeL [auth lL]210Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11, putativeM [auth lM]174Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13, putativeN [auth lN]291Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13, putativeO [auth lO]204Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14, putativeP [auth lP]135Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Find proteins for C4M6S2 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15Q [auth lQ]204Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17, putativeR [auth lR]179Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Find proteins for C4LX05 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18, putativeS [auth lS]167Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Find proteins for C4LXC8 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aT [auth lT]173Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19U [auth lU]198Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21, putativeV [auth lV]165Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Find proteins for C4LV69 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL22W [auth lW]137Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23, putativeX [auth lX]140Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23A, putativeY [auth lY]121Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24, putativeZ [auth lZ]163Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26, putativeAA [auth la]213Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27, putativeBA [auth lb]139Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15ACA [auth lc]148Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29DA [auth ld]64Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30, putativeEA [auth le]109Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31, putativeFA [auth lf]150Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32, putativeGA [auth lg]134Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34, putativeHA [auth lh]137Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
uL29IA [auth li]122Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35a, putativeJA [auth lj]108Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36, putativeKA [auth lk]104Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-A, putativeLA [auth ll]77Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37A, putativeMA [auth lm]93Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38, putativeNA [auth ln]88Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L39, putativeOA [auth lo]50Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40, putativePA [auth lp]56Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L44, putativeQA [auth lq]98Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4LS99 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
nascent polypeptide (Unk)RA [auth ls]14Entamoeba histolytica HM-1:IMSSMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25SA [auth sA]137Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26TA [auth sB]144Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS27UA [auth sC]83Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28, putativeVA [auth sD]69Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S29, putativeWA [auth sE]55Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta 2-like 1, putativeXA [auth sG]321Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2BB [auth sb]254Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5CB [auth sc]255Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3DB [auth sd]244Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1EB [auth se]256Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, putativeFB [auth sf]326Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7GB [auth sg]206Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6HB [auth sh]266Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7IB [auth si]201Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8JB [auth sj]237Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4KB [auth sk]185Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10, putativeLB [auth sl]127Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11, putativeMB [auth sm]156Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12, putativeNB [auth sn]136Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4LSC4 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13, putativeOB [auth so]150Entamoeba 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: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S14, putativePB [auth sp]146Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15, putativeQB [auth sq]144Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for C4M0C6 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15a, putativeRB [auth sr]129Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16, putativeSB [auth ss]157Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
Find proteins for B1N316 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17, putativeTB [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: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13UB [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: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19VB [auth sv]155Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10WB [auth sw]118Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21XB [auth sx]86Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23, putativeYB [auth sy]141Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24, putativeZB [auth sz]140Entamoeba histolytica HM-1:IMSSMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
25S rRNAA [auth lA]3,503Entamoeba histolytica HM-1:IMSS
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Entity ID: 2
MoleculeChains LengthOrganismImage
5.8SB [auth lB]155Entamoeba histolytica HM-1:IMSS
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S rRNAC [auth lC]117Entamoeba histolytica HM-1:IMSS
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Entity ID: 51
MoleculeChains LengthOrganismImage
P-tRNAYA [auth sH]76Entamoeba histolytica HM-1:IMSS
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Entity ID: 52
MoleculeChains LengthOrganismImage
mRNAZA [auth sK]6Entamoeba histolytica HM-1:IMSS
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Entity ID: 53
MoleculeChains LengthOrganismImage
17S rRNAAB [auth sa]1,947Entamoeba histolytica HM-1:IMSS
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
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