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- PDB-9v29: Cryo- EM structure of small subunit (body) of 75S ribosome with A... -

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Basic information

Entry
Database: PDB / ID: 9v29
TitleCryo- EM structure of small subunit (body) of 75S ribosome with A/P- & P/E- tRNAs from Entamoeba histolytica bound to antibiotic paromomycin
Components
  • (40S ribosomal protein ...) x 9
  • (Small ribosomal subunit protein ...) x 5
  • 17S rRNA
  • A/P-tRNA
  • P/E-tRNA
  • Ribosomal protein S14, putative
  • mRNA
KeywordsRIBOSOME / SSU-body of 75S Ribosome-PAR complex / A/P-tRNA / P/E-tRNA / Entamoeba histolytica
Function / homology
Function and homology information


maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome ...maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / zinc ion binding / cytosol
Similarity search - Function
PUA domain profile. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S27e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus ...PUA domain profile. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S27e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / : / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S15 signature. / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / Ribosomal protein S11 / Ribosomal protein S11 / RNA-binding S4 domain superfamily / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Zinc-binding ribosomal protein / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
PAROMOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S13, putative / Ribosomal protein S14, putative / 40S ribosomal protein S15a, putative / 40S ribosomal protein S6 ...PAROMOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S13, putative / Ribosomal protein S14, putative / 40S ribosomal protein S15a, putative / 40S ribosomal protein S6 / 40S ribosomal protein S4, putative / 40S ribosomal protein S8 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S23, putative / Small ribosomal subunit protein eS1 / 40S ribosomal protein S26 / Small ribosomal subunit protein uS5 / 40S ribosomal protein S11, putative / 40S ribosomal protein S7 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS27
Similarity search - Component
Biological speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSharma, S. / Mishra, S. / Gourinath, S. / Kaushal, P.S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR45101/DRUG/134/121/2022 India
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structure of ribosome from pathogenic protozoa Entamoeba histolytica reveals unique features of its architecture.
Authors: Shivani Sharma / Shalini Mishra / Samudrala Gourinath / Prem S Kaushal /
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 ...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.
History
DepositionMay 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
sB: 40S ribosomal protein S26
sC: Small ribosomal subunit protein eS27
sI: A/P-tRNA
sJ: P/E-tRNA
sK: mRNA
sa: 17S rRNA
sb: Small ribosomal subunit protein uS2
sc: Small ribosomal subunit protein uS5
se: Small ribosomal subunit protein eS1
sf: 40S ribosomal protein S4, putative
sh: 40S ribosomal protein S6
si: 40S ribosomal protein S7
sj: 40S ribosomal protein S8
sk: Small ribosomal subunit protein uS4
sm: 40S ribosomal protein S11, putative
so: 40S ribosomal protein S13, putative
sp: Ribosomal protein S14, putative
sr: 40S ribosomal protein S15a, putative
sy: 40S ribosomal protein S23, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,011,19920
Polymers1,010,58319
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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40S ribosomal protein ... , 9 types, 9 molecules sBsfshsisjsmsosrsy

#1: Protein 40S ribosomal protein S26


Mass: 16455.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M7G9
#10: Protein 40S ribosomal protein S4, putative


Mass: 36830.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LYF4
#11: Protein 40S ribosomal protein S6


Mass: 29822.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LXN2
#12: Protein 40S ribosomal protein S7


Mass: 21999.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M9F9
#13: Protein 40S ribosomal protein S8


Mass: 27031.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M0Q2
#15: Protein 40S ribosomal protein S11, putative


Mass: 18248.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M979
#16: Protein 40S ribosomal protein S13, putative


Mass: 17038.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: A0A175JJM9
#18: Protein 40S ribosomal protein S15a, putative


Mass: 14692.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LXM0
#19: Protein 40S ribosomal protein S23, putative


Mass: 15745.536 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M5B7

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Small ribosomal subunit protein ... , 5 types, 5 molecules sCsbscsesk

#2: Protein Small ribosomal subunit protein eS27 / 40S ribosomal protein S27 / EHZC3 protein


Mass: 9338.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: P38654
#7: Protein Small ribosomal subunit protein uS2


Mass: 28633.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M5A0
#8: Protein Small ribosomal subunit protein uS5 / 40S ribosomal protein S2


Mass: 27737.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M7U0
#9: Protein Small ribosomal subunit protein eS1


Mass: 29094.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M609
#14: Protein Small ribosomal subunit protein uS4 / 40S ribosomal protein S9


Mass: 21548.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: O15612

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RNA chain , 4 types, 4 molecules sIsJsKsa

#3: RNA chain A/P-tRNA


Mass: 24484.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
#4: RNA chain P/E-tRNA


Mass: 24617.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
#5: RNA chain mRNA


Mass: 3193.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
#6: RNA chain 17S rRNA


Mass: 628401.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: GenBank: BDEQ01000001

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Protein / Non-polymers , 2 types, 2 molecules sp

#17: Protein Ribosomal protein S14, putative


Mass: 15670.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: B1N2I3
#20: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H45N5O14 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of SSU body of 75S ribosome bound to Paromomycin with A/P and P/E-tRNA from Entamoeba histolytica
Type: RIBOSOME / Entity ID: #1-#19 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote) / Cellular location: cytoplasmic / Organelle: Ribosome
Buffer solutionpH: 7.4
Details: 20nM HEPES-sodium salt buffer pH 7.4, 100mM Potassium acetate, 10mM Magnesium acetate, 10mm Ammonium acetate, 3mM DTT
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 290 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 75000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 1.09 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 4688

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Processing

EM software
IDNameVersionCategory
1RELION3.1.4particle selection
2EPUimage acquisition
4CTFFINDCTF correction
7Cootmodel fitting
9RELION3.1.4initial Euler assignment
10RELION3.1.4final Euler assignment
11RELION3.1.4classification
12RELION3.1.43D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 54889
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37355 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 35.18 / Protocol: FLEXIBLE FIT / Space: REAL / Details: phenix.real_space_refinement
Atomic model building
ID 3D fitting-IDDetailsSource nameType
11the coordinates of 75S with P-tRNA was usedOtherother
21the coordinates of 75S with P-tRNA was usedOtherother

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