[English] 日本語
Yorodumi
- PDB-9v28: Cryo- EM structure of small subunit (head) of 75S ribosome with A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9v28
TitleCryo- EM structure of small subunit (head) of 75S ribosome with A/P- & P/E- tRNAs from Entamoeba histolytica
Components
  • (40S ribosomal protein ...) x 8
  • (Small ribosomal subunit protein ...) x 3
  • 17S rRNA
  • Ribosomal protein S29, putative
KeywordsRIBOSOME / SSU-head of 75S Ribosome / A/P-tRNA / P/E-tRNA / Entamoeba histolytica
Function / homology
Function and homology information


inositol hexakisphosphate binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / ribosome ...inositol hexakisphosphate binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. ...Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S19A/S15e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S14/S29 / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / K homology domain-like, alpha/beta / Ribosomal protein S13-like, H2TH / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S5 domain 2-type fold, subgroup / Winged helix DNA-binding domain superfamily / Ribosomal protein S5 domain 2-type fold / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S3 / 40S ribosomal protein S10, putative / Ribosomal protein S29, putative / 40S ribosomal protein S28, putative / 40S ribosomal protein S17, putative ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S3 / 40S ribosomal protein S10, putative / Ribosomal protein S29, putative / 40S ribosomal protein S28, putative / 40S ribosomal protein S17, putative / 40S ribosomal protein S16, putative / Small ribosomal subunit protein uS10 / 40S ribosomal protein S15, putative / 40S ribosomal protein S25 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS13
Similarity search - Component
Biological speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
sA: 40S ribosomal protein S25
sD: 40S ribosomal protein S28, putative
sE: Ribosomal protein S29, putative
sa: 17S rRNA
sd: 40S ribosomal protein S3
sg: Small ribosomal subunit protein uS7
sl: 40S ribosomal protein S10, putative
sq: 40S ribosomal protein S15, putative
ss: 40S ribosomal protein S16, putative
st: 40S ribosomal protein S17, putative
su: Small ribosomal subunit protein uS13
sv: Small ribosomal subunit protein eS19
sw: 40S ribosomal protein S20, putative


Theoretical massNumber of molelcules
Total (without water)818,34613
Polymers818,34613
Non-polymers00
Water00
1


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

-
Components

-
40S ribosomal protein ... , 8 types, 8 molecules sAsDsdslsqssstsw

#1: Protein 40S ribosomal protein S25


Mass: 14794.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M9F4
#2: Protein 40S ribosomal protein S28, putative


Mass: 7745.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LZQ8
#5: Protein 40S ribosomal protein S3


Mass: 26977.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LT02
#7: Protein 40S ribosomal protein S10, putative


Mass: 14575.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LVC0
#8: Protein 40S ribosomal protein S15, putative


Mass: 16405.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M7H3
#9: Protein 40S ribosomal protein S16, putative


Mass: 17547.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M2R7
#10: Protein 40S ribosomal protein S17, putative


Mass: 13617.970 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M0Z2
#13: Protein 40S ribosomal protein S20, putative


Mass: 13258.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4M5V7

-
Small ribosomal subunit protein ... , 3 types, 3 molecules sgsusv

#6: Protein Small ribosomal subunit protein uS7 / 40S ribosomal protein S5


Mass: 23072.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: O15587
#11: Protein Small ribosomal subunit protein uS13 / 40S ribosomal protein S18


Mass: 17698.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: P48151
#12: Protein Small ribosomal subunit protein eS19 / 40S ribosomal protein S19


Mass: 17776.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: O15631

-
Protein / RNA chain , 2 types, 2 molecules sEsa

#3: Protein Ribosomal protein S29, putative


Mass: 6472.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Entamoeba histolytica HM-1:IMSS (eukaryote)
References: UniProt: C4LW10
#4: 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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Cryo-EM structure of SSU-head of 75S ribosome with A/P and P/E-tRNA from Entamoeba histolytica
Type: RIBOSOME / Entity ID: all / 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

-
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: 1.106 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 11840

-
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: 142247
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39958 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 56.93 / 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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more